Often this is caused by having too many records and your server can't handle it, and files tend to get munged in the process of having multiple read-writes going on simultaneously (even with file locking, it happens...). Another posibility is that the other user is manually entering in the ID numbers, which I believe would also cause the linksid file to reset.
If you can afford it, you should really consider upgrading your license to Gossamer Links 3.x. Better performance, security, and much less problems in comparison to flat-file database formats.
Limecat is not pleased.