Other possibilities:

1.  Rebuild sort files on bank rec.

2.  Someone is deleting items out of bank rec.   Only way to check this is to compare g/l posting to bank rec postings (use the general ledger detail report and the bank recap report).

3.  Compare ending running balances from prior month to starting balance in current month.

I have had similar problems.  I'm assuming from the fact that you are talking about G/L and not about the bank statement that Bank Rec. is reconciling with the Bank Statement.  In that case the problem is in G/L.  The only way I found to localize that is start from a date when it reconciled.  Run Bank Rec. for a month with a date range filter, no start date but put the end date as the Bank Statement date.  G/L then should reconcile for that date with the adjusted balance at the bottom of the Bank Rec. report.  If it doesn't make it.  Then check it monthly.  

When it goes off if the normal suspects don't reveal a problem run a General Leger detail report and export that to Excel.  Go through that manually matching each G/L entry are group of entries to a line on the Bank Rec. report.  That is alot of work but will localize the problem.  After that how to prevent it depends on the exact nature of the problem.  Last time I had to do this the problem was data corruption and we needed our reseller to fix it.  

NIcholas

Please note that postings to the GL using General Ledger Journal Entry will NOT post to Bank Rec. People often make the mistake of entering entries there which thows off the Bank Rec.