I have by several people heard of a bug that if u resume a file over and over it well get corrupted, I personally have never seen it, and deliberately even tried to cause it, resumeing and cancling a file 100's of times, from 4 different people.
I couldnt make a single byte of the file bad, I was however resuming from MIRC clients only, and i sometimes wonder if the info on DCC RESUME has been missunderstood by some client other than mirc, even mircs help initially IMO misslabels it (but then 4 lines later states it exact meaning).
ie: PRIVMSG User1 : DCC RESUME filename port position
Position stands for not the position in the file it wants a resume from, but the length of the file it currently has (as in has up to this POSITION)
a non mirc client may beleive this is where to send from, giving you a file one byte out from where its ment to be.
I would suggest you take one of these files you have that is wrong, and in dos type
FC/B GOODCOPY.EXT BADCOPY.EXT
This well list you all differences in the file and there location (zero based), does the file have a block of data bad?, or does the data desync in the file (one byte appears to have moved up or down a byte).
I cant do this as i cant reproduce the error.