Just heard about this issue on Sage MAS 90 and MAS 200 and thought it may help someone in a similar situation.

MAS90 Purchases Clearing Won’t Foot

A client (version 4.3) reported to me that when the report did not tie to GL,
they manually added up the totals on the Purchases Clearing report. Their total
differs from the report total (and does balance to GL). I verified by exporting
the report to Excel and running a total. Sure enough, client is right.

Workaround

No KBA. Sage knows about it, but because it hasn’t verified by Engineering, it
is not available on the KnowledgeBase. Workaround is to run the Purchases
Clearing by Product Line report, which produces an accurate total.

via: Barbara Goldstein – Quanterasystems – San Jose California MAS 90 Reseller