DXTFixerX is a very handy program you all should know about.
It detects texture files with "bad" alpha channels and fixes them so they display properly in FS.

One odd thing I have found , if you clone your old drive as a back-up or to move it to newer media (ie, hard drive to SSD) you should re-run DXTFixerX again to verify
if all those texture files are still "fixed".

I found this out by mistake when I wanted to add some new re-paints. Instead of only scanning the new stuff I accidently scanned my entire FS9 install and found something like 150 textures which needed to be repaired. I know these files were already fixed on the older drive. I also checked my FS2002 install and found some more textures to fix.

So, if you're in doubt, re-run DXTFixerX every now and then.