I'm a new member that just joined and downloaded the June 1st trainer yesterday, so I definitely have the latest version.
I did find a workaround though: If you have at least one (or maybe 2) "Stop Worm" in your inventory, the "Freeze Hack Timer" option will freeze the countdown timer for that and that will stop the progress for the hacking countdown indefinitely. If you use that with "Unl. Ammo/Dupe Wpn Addons" option, it will also keep your "Stop Worms" from being used up, so you can still get unlimited hacking time, it's just a little bit more complicated.
This is definitely the easiest way to go. Unlimited grenades/items option means that once you have 1 multitool you'll never lose it. Some people might think it's not working but just remember to hold down left mouse and eventually it'll unlock it. The higher level security locks/computers take longer to unlock.
Please delete your current trainer, wipe your browser cache/Windows temp folder, reboot your PC, download the latest trainer, run it with admin rights and try again.
Please let the Steam client update your legally purchased game to the latest version and use our latest trainer.