If you wanted skill points, why didn't you just use cheats?

So...it let you save the game after exploiting the glitch, but after you reload your save, it won't let you save again? Even immediately? That sounds a bit odd. It could be a glitched save file.

Let's rule out the simplest cause. Maybe you have to click it an odd number of times. So click the panel again for another 100 skill points and see if it lets you save then. If not, reload and click it twice and see if that works.

I doubt it's because you have too many skill points, since the skill points cheat gives you way more. But just in case, let's try to rule it out by changing your skill points.

Press "T" to open the console, delete everything on the line and enter the command "Set DeusEx.JCDentonMale bCheatsEnabled True". Then enter the command "allskillpoints". This will give you over 100,000 skill points. See if that helps.

That probably didn't work, so enable cheats again and enter the command "legend". It will open up a menu that will allow you to edit flags. Check if there are any suspicious flags there. This step might be hard, so you could skip to the next one.

Have you tried leaving that map and making the game load another part of Vandenberg? You could also try reloading that map. Enable cheats and type "open 12_Vandenberg_Tunnels". The most rigorous solution would involve reloading the map and messing about with your flags.

If it's a glitched save file...just grab your friend's save file and use cheats to get back your gear. Or replay from Hell's Kitchen now that you know where everything is. You can enable God mode to rush through the levels and use cheats to give yourself better equipment that you miss from not exploring everything.