I first noticed this after migrating from 2004P to 2006P.
I hold treasury bills with the same CUSIPs in two different investment accounts. The first is a 6-month bill, the second is a 3-month bill of the same issue. I track these with the last three characters of the CUSIP for the securities symbol..
When I bought the latest bill, the account holding the earlier issue of the same bill estimated it's value using the new price. That results in an error in the securities value indicated by Quicken and also sees it as a gain because the cost basis is not equal to the estimated price.
I deleted the new account, purged the older account of all transactions using that CUSIP and deleted the CUSIP from the securities list. After that I ran re-entered the transactions in the older register and used ctl Z to recalculate. That did not fix the problem.
My eventual workaround was to append the words "event 1" to the symbol for the first bill . That works but it took a lot of time to arrive at that approach. Perhaps there is a better way?
I restored an earlier image of the entire drive to confirm that the problem also existed in Q2004.
The YTD performance bugs have also carried forward to Q2006.
In spite of these bugs, there are enough improvements in the program that I will keep it.