There is a bug in the current version of FastCheck that means recently created folders will not be checked correctly. Eric has released a new version of FastCheck that corrects this bug. You can download it here:
http://www.fastcheck.org/download/FastCheck_1_0_13_5.exe
After downloading and running this new version, you have to go to the Options page, and to the Accounts list, double click on your account and enter your password twice to force a refresh of the folder list.