I know this response is late--but I think it's a very relevant question. Our main issues with the conversion involved membership. The way Giftmaker reads memberships (specifically upgrades and downgrades) is different than how Raiser's Edge reads them. Raiser's Edge only allows one membership at a time--only one line at a time. Giftmaker creates different lines for each membership type-each time you upgrade or downgrade. So, when you convert to Raiser's Edge--it acts as if you have several different memberships. This messes with reports and queries, and membership cards.
Each time I renew a membership, I need to double check to make sure there is only one membership per record. This might not be a big deal for some organizations, but it messes with some very important queries for us. Plus we have a few minor issues with the differences in printing membership cards. Best of Luck in your conversions!