White rectangles instead of transparency

Hello all,
I am a beginnger in InDesign - what a great tool!
I get white rectangles instead of transparency when exported as (any version of) PDF or printed, but fine when exported as JPEG. I am using a 3rd party template
Using InDesign 6.0
Thank you,
Blackbird

Hello Peter, thank you for rapid reply.
I am having white box effect. It is around the imported .ai files (which do not scale properly as well - another problem). See screenshot (ignore the font mismatch):
http://img20.imageshack.us/img20/8122/screenshotfrom201209041.png
I assume it can be fixed as the third party company who provided this template were able to export it smoothly to a PDF (see image above, rightmost screenshot)
I tried remedies from the link you gave, no change/luck:
* Overprint preview (not available in Acrobat Reader 10 anymore)
* Simulate overprint (and print it to PDF via CutePDF Writer) - same white boxes
* Transparency flattener set to all-raster - same white boxes
I have "Coated FOGRA27" CMYK profile, instead of the workspace's default "US Web Coated SWOP v2", I set Id CS6.0 to "Preserve Embedded Profiles" - still white boxes
Hope you can help, before I finally attempt to contact the 3rd party company (they are not overly helpful/available as you are)
Thank you,
Blackbird

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MPlayer SVN-r31303-4.5.0 (C) 2000-2010 MPlayer Team
CPU vendor name: GenuineIntel max cpuid level: 10
CPU: Intel(R) Core(TM)2 CPU 6400 @ 2.13GHz (Family: 6, Model: 15, Stepping: 2)
extended cpuid-level: 8
extended cache-info: 134242368
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Reading /home/cinan/.mplayer/codecs.conf: Can't open '/home/cinan/.mplayer/codecs.conf': No such file or directory
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init_freetype
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Setting up LIRC support...
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mplayer: No such file or directory
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get_path('V.2009.S01E04.Its.Only.the.Beginning.HDTV.XviD-FQM.avi.conf') -> '/home/cinan/.mplayer/V.2009.S01E04.Its.Only.the.Beginning.HDTV.XviD-FQM.avi.conf'
Playing /media/data/download/V.2009.S01E04.Its.Only.the.Beginning.HDTV.XviD-FQM.avi.
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[file] File size is 367449578 bytes
STREAM: [file] /media/data/download/V.2009.S01E04.Its.Only.the.Beginning.HDTV.XviD-FQM.avi
STREAM: Description: File
STREAM: Author: Albeu
STREAM: Comment: based on the code from ??? (probably Arpi)
LAVF_check: AVI format
AVI file format detected.
list_end=0x146
======= AVI Header =======
us/frame: 41708 (fps=23.976)
max bytes/sec: 0
padding: 0
MainAVIHeader.dwFlags: (272) HAS_INDEX IS_INTERLEAVED
frames total: 59292 initial: 0
streams: 2
Suggested BufferSize: 0
Size: 624 x 352
==========================
list_end=0xD4
==> Found video stream: 0
[aviheader] Video stream found, -vid 0
====== STREAM Header =====
Type: vids FCC: XVID (44495658)
Flags: 0
Priority: 0 Language: 0
InitialFrames: 0
Rate: 23976024/1000000 = 23.976
Start: 0 Len: 59292
Suggested BufferSize: 127506
Quality 0
Sample size: 0
==========================
Found 'bih', 40 bytes of 40
======= VIDEO Format ======
biSize 40
biWidth 624
biHeight 352
biPlanes 1
biBitCount 24
biCompression 1145656920='XVID'
biSizeImage 658944
===========================
Regenerating keyframe table for MPEG-4 video.
list_end=0x146
==> Found audio stream: 1
[aviheader] Audio stream found, -aid 1
====== STREAM Header =====
Type: auds FCC: (0)
Flags: 0
Priority: 0 Language: 0
InitialFrames: 0
Rate: 48000/1152 = 41.667
Start: 0 Len: 103039
Suggested BufferSize: 0
Quality 0
Sample size: 0
==========================
Found 'wf', 30 bytes of 18
======= WAVE Format =======
Format Tag: 85 (0x55)
Channels: 2
Samplerate: 48000
avg byte/sec: 16000
Block align: 1152
bits/sample: 16
cbSize: 12
mp3.wID=1
mp3.fdwFlags=0x2
mp3.nBlockSize=1152
mp3.nFramesPerBlock=1
mp3.nCodecDelay=0
==========================================================================
list_end=0x16A
hdr=Software size=16
Software : transcode-1.0.4
list_end=0x15BF3432
Found movie at 0x800 - 0x15BF3432
Reading INDEX block, 162331 chunks for 59292 frames (fpos=364852282).
AVI index offset: 0x0 (movi=0x800 idx0=0x800 idx1=0x11C66)
Auto-selected AVI video ID = 0
Auto-selected AVI audio ID = 1
AVI: Searching for audio stream (id:1)
XXX initial v_pts=0.000 a_pos=0 (0.000)
AVI video size=322223780 (59292) audio size=41298048 (103039)
VIDEO: [XVID] 624x352 24bpp 23.976 fps 1042.4 kbps (127.2 kbyte/s)
Auto-selected AVI audio ID = 1
[V] filefmt:3 fourcc:0x44495658 size:624x352 fps:23.976 ftime:=0.0417
Clip info:
Software: transcode-1.0.4
get_path('sub/') -> '/home/cinan/.mplayer/sub/'
[file] File size is 36608 bytes
STREAM: [file] /media/data/download/V S01E04.srt
STREAM: Description: File
STREAM: Author: Albeu
STREAM: Comment: based on the code from ??? (probably Arpi)
SUB: Detected subtitle file format: subviewer
SUB: opened iconv descriptor.
SUB: closed iconv descriptor.
SUB: Read 503 subtitles, 0 bad line(s).
SUB: Adjusted 84 subtitle(s).
SUB: Added subtitle file (1): /media/data/download/V S01E04.srt
[vo_vaapi] Using OpenGL rendering
X11 opening display: :0.0
vo: X11 color mask: FFFFFF (R:FF0000 G:FF00 B:FF)
vo: X11 running at 1680x1050 with depth 24 and 32 bpp (":0.0" => local display)
[x11] Detected wm supports NetWM.
[x11] Detected wm supports FULLSCREEN state.
[x11] Detected wm supports ABOVE state.
[x11] Detected wm supports BELOW state.
[x11] Current fstype setting doesn't honour any X atoms
libva: libva version 0.31.1-sds1
Xlib: extension "XFree86-DRI" missing on display ":0.0".
libva: va_getDriverName() returns 0
libva: Trying to open /usr/lib/va/drivers/fglrx_drv_video.so
libva: va_openDriver() returns 0
==========================================================================
Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family
[VD_FFMPEG] VA API accelerated codec.
Unsupported PixelFormat 61
[VD_FFMPEG] Trying pixfmt=1.
[ffmpeg] aspect_ratio: 0.000000
VDec: vo config request - 624 x 352 (preferred colorspace: MPEG-4 VA-API Acceleration)
Trying filter chain: vo
VDec: using MPEG-4 VA-API Acceleration as output csp (no 0)
Movie-Aspect is undefined - no prescaling applied.
VO Config (624x352->624x352,flags=0,'MPlayer',0x56410020)
VO: [vaapi] 624x352 => 624x352 MPEG-4 VA-API Acceleration
VO: Description: VA API with X11
VO: Author: Gwenole Beauchesne <[email protected]>
[vo_vaapi] Using 1:1 VA surface mapping
FATAL: Cannot initialize video driver.
Unsupported PixelFormat 61
[VD_FFMPEG] Trying pixfmt=0.
[ffmpeg] aspect_ratio: 0.000000
Unsupported PixelFormat 61
VDec: vo config request - 624 x 352 (preferred colorspace: Unknown 0x0000)
Trying filter chain: vo
Could not find matching colorspace - retrying with -vf scale...
Opening video filter: [scale]
SwScale params: -1 x -1 (-1=no scaling)
Trying filter chain: scale vo
The selected video_out device is incompatible with this codec.
Try appending the scale filter to your filter list,
e.g. -vf spp,scale instead of -vf spp.
[VD_FFMPEG] Trying pixfmt=2.
[ffmpeg] aspect_ratio: 0.000000
VDec: vo config request - 624 x 352 (preferred colorspace: MPEG-4 Part 2 VDPAU acceleration)
Trying filter chain: vo
Could not find matching colorspace - retrying with -vf scale...
Opening video filter: [scale]
SwScale params: -1 x -1 (-1=no scaling)
Trying filter chain: scale vo
The selected video_out device is incompatible with this codec.
Try appending the scale filter to your filter list,
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[VD_FFMPEG] Trying pixfmt=3.
[ffmpeg] aspect_ratio: 0.000000
VDec: vo config request - 624 x 352 (preferred colorspace: Planar YV12)
Trying filter chain: vo
VDec: using Planar YV12 as output csp (no 2)
Movie-Aspect is undefined - no prescaling applied.
VO Config (624x352->624x352,flags=0,'MPlayer',0x32315659)
VO: [vaapi] 624x352 => 624x352 Planar YV12
VO: Description: VA API with X11
VO: Author: Gwenole Beauchesne <[email protected]>
INFO: libavcodec init OK!
Selected video codec: [ffodivx] vfm: ffmpeg (FFmpeg MPEG-4)
==========================================================================
==========================================================================
Opening audio decoder: [mp3lib] MPEG layer-2, layer-3
dec_audio: Allocating 4608 + 65536 = 70144 bytes for output buffer.
mp3lib: using SSE optimized decore!
MP3lib: init layer2&3 finished, tables done
MPEG 1.0, Layer III, 48000 Hz 128 kbit Stereo, BPF: 384
Channels: 2, copyright: No, original: Yes, CRC: No, emphasis: 0
AUDIO: 48000 Hz, 2 ch, s16le, 128.0 kbit/8.33% (ratio: 16000->192000)
Selected audio codec: [mp3] afm: mp3lib (mp3lib MPEG layer-2, layer-3)
==========================================================================
Building audio filter chain for 48000Hz/2ch/s16le -> 0Hz/0ch/??...
[libaf] Adding filter dummy
[dummy] Was reinitialized: 48000Hz/2ch/s16le
[dummy] Was reinitialized: 48000Hz/2ch/s16le
Trying preferred audio driver 'alsa', options '[none]'
alsa-init: requested format: 48000 Hz, 2 channels, 9
alsa-init: using ALSA 1.0.23
alsa-init: setup for 1/2 channel(s)
alsa-init: using device default
alsa-init: pcm opened in blocking mode
alsa-init: got buffersize=32768
alsa-init: got period size 1024
alsa: 48000 Hz/2 channels/4 bpf/32768 bytes buffer/Signed 16 bit Little Endian
AO: [alsa] 48000Hz 2ch s16le (2 bytes per sample)
AO: Description: ALSA-0.9.x-1.x audio output
AO: Author: Alex Beregszaszi, Zsolt Barat <[email protected]>
AO: Comment: under developement
Building audio filter chain for 48000Hz/2ch/s16le -> 48000Hz/2ch/s16le...
[dummy] Was reinitialized: 48000Hz/2ch/s16le
[dummy] Was reinitialized: 48000Hz/2ch/s16le
Starting playback...
Increasing filtered audio buffer size from 0 to 34816
[ffmpeg] aspect_ratio: 1.772727
VDec: vo config request - 624 x 352 (preferred colorspace: Planar YV12)
Trying filter chain: vo
VDec: using Planar YV12 as output csp (no 2)
Movie-Aspect is 1.77:1 - prescaling to correct movie aspect.
VO Config (624x352->624x352,flags=0,'MPlayer',0x32315659)
VO: [vaapi] 624x352 => 624x352 Planar YV12
VO: Description: VA API with X11
VO: Author: Gwenole Beauchesne <[email protected]>
*** [vo] Allocating (slices) mp_image_t, 624x352x12bpp YUV planar, 329472 bytes
*** [vo] Allocating (slices) mp_image_t, 624x352x12bpp YUV planar, 329472 bytes
Unicode font: 654 glyphs.
Unicode font: 654 glyphs.
*** [vo] Allocating (slices) mp_image_t, 624x352x12bpp YUV planar, 329472 bytes
Uninit audio filters... 0.004 ct: -0.026 28/ 28 12% 8% 0.5% 1 0
[libaf] Removing filter dummy
Uninit audio: mp3lib
Uninit video: ffmpeg
alsa-uninit: pcm closed
vo: uninit ...

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