Chad,
I should have provided some better information the first time around.
I attempted to clear all the conflicts on 6/2/12- They reappeared.
Our transaction history sync is set to 60 days.
We keep previous year information in our active QB file. So the archiving had to do with all transactions prior to 12_31_10.
I have also tried to perform a full-sync and without fail during the checking invoices stage, QuickBooks produces a message that it need to shut down and thus the sync doesn't complete.