I would assume you installed a mod first but in the base game yes you should be able to put another pip into short swords

You can't fix it. Unfortunately, you misunderstood how dual classing works.

Once dual classed, you can only put proficiency points in accordance to the rules of the NEW class. Once you surpass your original class in level, it will simply give you benefits of whatever you had before the switch, but you won't be able to put further points into the same proficiency unless your new class can progress in it, too.

In other words, it would have worked if you switched from thief to a fighter, but not vice versa. If you wanted to have 4 or even 5 points in a weapon (a common strategy when dual-classing from a fighter), you should have done it before you switched to thief. You can fix this with EE Keeper, if you do not wish to start over, or simply live with it.

Actually You're wrong. I installed Tweak packs and some of tweaks i seected was nerfing dual classing. After reinstalling game and choosing very few tweaks (e.g. no helmets and nothing else) i couldve improve my proficiences to 5 stars in long swords and short ones thereafter.

I stand corrected. I had the same pack, too. It works as you described in the original game, I believe that the way I described it is per PnP. Glad to hear you were able to fix it.