Things to investigate:
1) Are there unposted GL transactions? Look in the Financial > General Journal. Are there related transactions there?
2) Look at your posting setup. Are Post To and Post Through GL, either one marked? If neither one is marked, then no GL entry is created.
3) The only way that you will get DR-Exp, CR-Cash is to cut the check at the time of Invoice entry. The typical process is to do Invoice Entry (DR-Exp, CR-AP). Then do a select checks to cut the checks, (DR-AP, CR-Cash). Is it possible that the Expenses were recognized in a different period than the check payments? You need to understand the process used to trouble shoot.
There are some other possibilities, but they are really just refinements of the about 3 things to look at.
Warren.