My issue is that these transactions do not exist in the blockchain and were generated during a split. The transactions that are showing on blockchain.info do not appear in my wallet... weird issue. I imagine that rebuilding a new wallet from the private keys should fix it though, since it re-verifies every transaction for every private key imported.
I just realised - you're importing the keys and rescanning the whole blockchain for each one aren't you. No wonder it's taking so long.
If you want to speed it up, and are comfortable building bitcoin-qt from source, comment out these two lines in src/rpcdump.cpp then rebuild:
pwalletMain->ScanForWalletTransactions(pindexGenesisBlock, true);
pwalletMain->ReacceptWalletTransactions();
Then you'll be able to import all your private keys very quickly, like less than a second each. Then run a single 'bitcoin-qt -rescan' at the end and you're done.
There's no need to rescan the wallet separately for every key you import, but that's what bitcoin-qt does.