I had a similar problem with Pocket Quicken that lets me sync my Palm IIIxe with Quicken on my desktop. Watch that the transactions you're losing arent't being reconciled with an already reconciled entry.
Select any "match" item and check on your register that it's matched to the correct register entry. If it's not, click "unmatch" and keep pressing "unmatch" until it either displays the correct entry or puts it in as a new one.
There's mention of this on Pocket Quicken's web site but of course, it's not on the Intuit site. I've never had any luck with Quicken or Intuit's support staff.