Hi, Are you sure you are looking at the correct GL accounts? Do an enquiry on the purchasing invoice and check its distributions to make sure they are as you expect.
Are the purchasing invoices actually poted? or can you still open them in the transaction entry window? Perhaps some of the PM transactions in the batch were rejected for some reason (ie they did not post)...If the batch is still available, print an edit list for it...check if your invoices are listed and what the error message is.
Did the GL journals actually post? Click on Transactions >> Financial >> General Journal...search through any unposted GL transactions and see if the postings created by the invoices are unposted.
If you're using GP 10, you can run the GL to PM reconciliation and see what this throws up.
Also check that these document types are set to post to GL (Setup >> Posting >> Posting).
Check the above first, and let us know how you get on.