A title search on "tonnage" will find many posts on this topic (ignore the NYGM ones!). Usual reasons for this stock SH3 problem are outlined in
http://www.subsim.com/radioroom/showthread.php?t=93381
Strangely, I have tried to replicate this problem myself (running stock SH3 and/or SH3Cmdr and/or GW and/or RUb) and have never been able to. :hmm:
I do know that the problem has existed since day 1 (the first post I found was dated back in April last year) and I have seen many early careers with the other telltale effect of this problem - missing career and flotilla *start* dates.
If it's possible, the only sure way to avoid this problem is to not save mid-patrol. Prolly not feasible for some though...