Yeah, I just did a request for update on that too. Once you start Tier One stuff, the supply requirements to do weapon upgrades is insane. Not being able to use the "set supply" option is a pain.
I'm sure he can fix it though or give us a blanket "set all supplies" button or a "free tier damage upgrade" button maybe? We'll see.
Just going into skills and highlighting the skill with the first required resourse, gave me that resourse, eg
need med, find skill with med as first needed resource, put the box around it and activate the options. (may have to leave the menu and activate.
This seemed to always work for me.
Try re-installing EAC.
I would need to see what's going on with your setup's, best thing to do is submit a support ticket and maybe request a teamviewer session. In the meantime now that you have everything re-installed, try following the PDF included to the letter, especially the last part,
Lastly, to revert the game and the installation back to normal, it's best practice to CLOSE THE GAME FIRST, and THEN close the trainer. This will allow the trainer to reset the game back to it's normal state to be able to be used WITHOUT A TRAINER for online play.