Audio drift on Constant framerate

Question

I am experiencing an audio drift problem on a specific set of videos when using Premiere Pro CC (2014) on Windows 7. The audio starts out well, but eventually drifts way out of sync. This already happens in the Source Monitor. I read that this can be due to the use of Variable framerate video. However, the video I have is Constant framerate. At first, I thought it might have been Premiere itself or my PC, but when I dropped a Blu-ray rip into Premiere, it worked perfectly. It turns out this happen consistently with all videos from the source website (Giant Bomb).
It seems to me Premiere misinterprets the footage. When I play the video in MPC-HC, the duration reads 2:51:10 but when I drop it into Premiere, it reports the duration as 2:51:00:03. I checked the Sequence settings, but they all seem to correspond with the source video. Even when I set it manually, it doesn't help.
Screenshot:
And here's the MediaInfo output:
General
Complete name : D:\Exchange\source\problem-file.mp4
Format : MPEG-4
Format profile : Base Media
Codec ID : isom
File size : 5.12 GiB
Duration : 2h 51mn
Overall bit rate mode : Variable
Overall bit rate : 4 281 Kbps
Writing application : Lavf55.19.104
Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : [email protected]
Format settings, CABAC : Yes
Format settings, ReFrames : 3 frames
Format settings, GOP : M=1, N=120
Codec ID : avc1
Codec ID/Info : Advanced Video Coding
Duration : 2h 51mn
Bit rate : 4 000 Kbps
Width : 1 280 pixels
Height : 720 pixels
Display aspect ratio : 16:9
Frame rate mode : Constant
Frame rate : 59.940 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.072
Stream size : 4.78 GiB (93%)
Writing library : x264 core 140
Encoding settings : cabac=1 / ref=3 / deblock=1:0:0 / analyse=0x1:0x111 / me=hex / subme=7 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=0 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=24 / lookahead_threads=4 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=0 / weightp=2 / keyint=120 / keyint_min=12 / scenecut=0 / intra_refresh=0 / rc_lookahead=40 / rc=abr / mbtree=1 / bitrate=4000 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / vbv_maxrate=8000 / vbv_bufsize=8000 / nal_hrd=none / filler=0 / ip_ratio=1.40 / aq=1:1.00
Language : English
Tagged date : UTC 2014-07-30 04:09:12
Audio
ID : 2
Format : AAC
Format/Info : Advanced Audio Codec
Format profile : LC
Codec ID : 40
Duration : 2h 51mn
Bit rate mode : Variable
Bit rate : 128 Kbps
Maximum bit rate : 8 000 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Compression mode : Lossy
Stream size : 157 MiB (3%)
Language : English
Tagged date : UTC 2014-07-30 04:09:12
Other #1
ID : 65536
Type : Hint
Format : RTP
Codec ID : rtp
Duration : 2h 51mn
Encoded date : UTC 2014-07-30 03:58:42
Tagged date : UTC 2014-07-30 04:09:12
Other #2
ID : 65537
Type : Hint
Format : RTP
Codec ID : rtp
Duration : 2h 51mn
Encoded date : UTC 2014-07-30 04:09:00
Tagged date : UTC 2014-07-30 04:09:12
Bit rate mode : VBR
Final note: Kdenlive under Linux seems to have no problem handling the video correctly.
Any ideas as to why this is happening?

Answer 1

Well, ladies and/or gentlemen, I am now content to call the file in my original post an anomaly. I downloaded two versions of a different video: one from Youtube and one from the site. Both worked fine and seemed perfectly synced up. Even the one from Youtube, which MediaInfo reports is Variable frame rate! That sort of blew my mind, as I expected that not to work. I then thought that the length might have something to do with it, so I downloaded another video of equal length and content (again with camera footage and gameplay footage). It was also synced. So there must just be some problem with the first file after all. I did spot some glitching in the video, so perhaps it's corrupted somewhere. Problem "solved" I suppose. Some additional notes/questions below. Thanks for your help in getting to the bottom of this mystery!
RoninEdits: Before doing all this, I tried your method. I made markers in the Source Monitor, but they didn't transfer to the timeline when I made a Sequence. I tried making those markers on the timeline itself, but then they didn't move when I used the Rate Stretch Tool. Do you have (a link to) instructions on how to properly do this? I'm a beginner in Premiere Pro and I couldn't figure it out.
J. Simon: I guess what I meant by standardized is that it fits the Base profile and 4.1 level standards of H.264. Incidentally, if I check the Sequence settings on the file that originate from the site -- the 60FPS HD files -- Premiere automatically assumes they are in fact AVC-Intra 100 720p. So maybe they did standardize these videos after all.