What version of Informatica are you using?
Do your session and/or workflow logs for the workflow and session(s) having the problem report any errors? You said there's something about missing records, but what is the specific message and where is it reported? I expect it'd be in your session logs.
Generally, when troubleshooting an Informtica issue, I'll start with the session logs. We're using v. 6 here and have noticed some issues with SQL Server (especially when using stored procedures--you're not using stored procedures to insert your data are you?). Have you enabled detailed logging in your sessions, to try to track down what's going on?