Tested on both Windows XP 32-bit and Windows 7 64-bit (both freshly installed, no other 3rd party software installed or running). Reasonably sure it's a relatively new bug, perhaps only introduced in last couple of versions:
How to reproduce:
1. Create a folder
2. Place EICAR test file (or other "malware" that EEK will usually detect) in the folder
3. Place a large file (eg. 500Mb video) into the same folder (that isn't "malware")
4. Run EEK.
Select "Scan", then "Custom Scan".
Ensure to remove all default listed directories to be scanned.
Also remove all checkboxes under "Scan Objects" (not necessary to reproduce this bug but will speed up the scan)
Select "Add folder"
Browser to the folder you created in step 1. above
5. Click "Next" to scan the folder
6. Notice that EEK doesn't detect the "malware"
7. Remove the large file from the folder
8. Repeat the scan of this folder as in steps 4-5
9. Notice that EEK now detects the "malware"
Can anyone else reproduce this? If so, can the devs take a look please? I like using EEK as my on-demand scanner, but I've lost some trust in it now.
One workaround is to scan the parent folder instead of the actual folder, but this sort of defeats the purpose of "Custom Scan".
Note I'm not sure how large a file it needs to be. A bit more testing reveals rather random behavior, with EEK detecting it sometimes and sometimes not, with various files within the folder. Quite bizarre. But pretty sure everyone should be able to reproduce it at least once if they follow the steps above carefully.