ITunes 6.0.3 destroyed my music files (mp3 and m4a).

iTunes 6.0.1 has destroyed a significant amount of my 35,000 song library. Not just the library, but the SONG FILES. Take a look:
http://riggswerks.com/itunes/diy_gaps.gif
This is an mp3 file that has been opened in Peak. See all those gaps? They were added by iTunes.
What happens is when a song that has been damaged like this goes to play, iTunes will only play it till its first gap (in the case of the screenshot song, about 2 seconds). Once it hits the gap, it moves on to the next song in the playlist. For some reason, iTunes is adding the gaps and duplicating small portions of the song in between the gaps, cutting off several seconds of the song ending, etc. So, it wouldn't be as simple as cutting out the gaps in a sound editing program, because song data has been added as well. The files are useless. I tried to upload one, but my ftp client wouldn't allow a file that severely damaged to be moved.
Two questions:
a) Is iTunes 6.0.1 safe to use? I'm scared to death that it will end up trashing more of my music, so I reverted to version 5, and locked my dedicated 250GB music hard drive. Anyone out there that can help explain what's going on would be tremendously helpful.
and
b) It seems that once there is a screwed up song in the iTunes library, it forces any overwritten file for the bad songs to adopt the gaps and characteristics of the previous version. For example, I reburned a couple of these bad songs from the original CD and selected for iTunes to replace the songs as they burned (after unlocking the hard drive)- when I went to play it, the new song- ripped straight from CD minutes before- had the same gapping problems. How can I reimport my good versions of these files if iTunes adopts the gaps and errors? I'm stuck.
For further reference (others have had similar/same issues):
http://discussions.apple.com/message.jspa?messageID=1308126#1308126
http://discussions.apple.com/message.jspa?messageID=1308121#1308121
http://discussions.apple.com/message.jspa?messageID=1308060#1308060
http://discussions.apple.com/message.jspa?messageID=1307909#1307909
For those who may know how to help- here's my set up:
PowerMac G5 Quad running 10.4.3
iTunes 6.0.1 (reverted back to iTunes 5 now)
TIA. core4

hiya!
hmmm. okay, here's a user tip on moving your music files to a different drive. can you spot anything you might have missed on the first attempt?
MacMuse: Move iTunes music/Library to new drive
love, b

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Microsoft Windows XP Professional Service Pack 3 (Build 2600)
INTEL_ DG41RQ__
iTunes 11.1.3.8
QuickTime 7.2
FairPlay 2.5.16
Apple Application Support 2.3.6
iPod Updater Library 11.1f5
CD Driver 2.2.3.0
CD Driver DLL 2.1.3.1
Apple Mobile Device 7.0.0.117
Apple Mobile Device Driver 1.64.0.0
Bonjour 3.0.0.10 (333.10)
Gracenote SDK 1.9.6.502
Gracenote MusicID 1.9.6.115
Gracenote Submit 1.9.6.143
Gracenote DSP 1.9.6.45
iTunes Serial Number 0012B9B00CB27BC0
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Video Display Information
ATI RADEON XPRESS 200 Series
Intel(R) G41 Express Chipset
**** External Plug-ins Information ****
No external plug-ins installed.
**** Network Connectivity Tests ****
Network Adapter Information
Adapter Name:        {E4F794BB-151F-490C-8AC0-1EDB6DA3718A}
Description:             D-Link DWA-125 Wireless N 150 USB Adapter(rev.A2) - Packet Scheduler Miniport
IP Address:              192.168.5.104
Subnet Mask:          255.255.255.0
Default Gateway:     192.168.5.1
DHCP Enabled:       Yes
DHCP Server:          192.168.5.1
Lease Obtained:      Sun Dec 22 21:35:11 2013
Lease Expires:         Mon Dec 23 21:35:11 2013
DNS Servers:          91.216.105.75
                                216.93.191.228
Active Connection: LAN Connection
Connected:              Yes
Online:                     Yes
Using Modem:         No
Using LAN:              Yes
Using Proxy:            No
Firewall Information
Windows Firewall is on.
iTunes is enabled in Windows Firewall.
Connection attempt to Apple web site was successful.
Connection attempt to browsing iTunes Store was successful.
Connection attempt to purchasing from iTunes Store was successful.
Connection attempt to iPhone activation server was successful.
Connection attempt to firmware update server was unsuccessful.
The network connection timed out.
Connection attempt to Gracenote server was successful.
iTunes has never successfully accessed the iTunes Store.
**** CD/DVD Drive Tests ****
No drivers in LowerFilters.
UpperFilters: GEARAspiWDM (2.2.3.0),
D: LITE-ON DVDRW SHW-160P6S, Rev PRS2
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**** Device Connectivity Tests ****
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Universal Serial Bus Controllers:
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Standard OpenHCD USB Host Controller
Standard OpenHCD USB Host Controller
Standard OpenHCD USB Host Controller
Standard OpenHCD USB Host Controller
Standard OpenHCD USB Host Controller
Intel(R) 82801G (ICH7 Family) USB Universal Host Controller - 27C8. Device is working properly.
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Intel(R) 82801G (ICH7 Family) USB Universal Host Controller - 27CA. Device is working properly.
Intel(R) 82801G (ICH7 Family) USB Universal Host Controller - 27CB. Device is working properly.
Intel(R) 82801G (ICH7 Family) USB2 Enhanced Host Controller - 27CC. Device is working properly.
FireWire (IEEE 1394) Host Controllers:
Texas Instruments OHCI Compliant IEEE 1394 Host Controller
Connected Device Information:
IPOD (K:\), iPod nano (7th Generation) running firmware version 1.0.2
Serial Number:         DCYK27TGF0GT
Bus Speed:              61440
**** Device Sync Tests ****
No iPod, iPhone, or iPad found.

Hi fkerrin!
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http://support.apple.com/kb/ht1351
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http://support.apple.com/kb/HT1364
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