You can log in to a Personal account and an Apps account simultaneously. Click on your account name (next to the tools icon top right) when logged in on one account, select "Switch account" and then "Sign in to another account", enter your second account details. Now you can switch in one window between the Apps account and Personal one by selecting "Switch account" again and then choosing which one to view. That's how I get around having an Apps and Personal account anyway.
The other problem here could be if, when you came on to Google Apps, you already had a matching personal account for that email address. e.g. Personal account with email of firstname.lastname@example.org and then you set up fred.com on Google Apps. Then, all your Personal accounts would have been moved to email@example.com, e.g. firstname.lastname@example.org to prevent any clashes... So you might need to use the +personal email address to log in to that account.