Problem: 

The 35mm mounted slides are being skewed by the Epson Scan software despite being aligned perfectly on the scanner.

Solution: 

1. Preview scan the slides. 
2. Create a marquee around all the slides you need to scan.
3. Select 'All' (button on the preview screen.)
4. Turn off Trimming (option underneath Target Size.)
5. Make sure everything else is unchecked (mask, dust removal, etc.)
6. Scan. Slides should no longer come out skewed.