Bank Reconciliation

I have two clients.  One is on Sage 300 ERP 2012 Premium PU2 and the other is on Accpac 100 6.0 PU1.  Both companies are using MS SQL 2008 R@ as their database engine. The 2012 client is using terminal services and the 6.0 client is on a local install with the data on a server.  When doing their bank reconciliation, clearing each entry will stall the system for up to 5 minutes per item.  Any ideas on what might be causing this issue?