Hi Indinera! I am experiencing exact the same issue. It starts to happen when Sarah hits level 32 in the Smuggler Warehouse.
After seeing this issue the first time, I tried recreating it with the last save file with which the allocation worked. I was able to recreate the bug in the same place where it first happened for me - in Smuggler Warehouse. But the first few level up allocations worked fine for Spark, Baretta, and Random in the same place. This issue persisted for me until I got to Western Shores, from Xen village (my current spot in the game).
I am sending you the following save files:
1. For before the bug occurred, "Save1.rxdata" - After sleeping in the Xen Inn to trigger Quest 14 (Find Guanidia), and after talking to the NPCs outside.
2. For right after the bug occurred, "Save2.rxdata" - Right after I got the issue again in Smuggler Warehouse. Here are the steps you can take with Save1.rxdata to recreate the Save2.rxdata save file:
a. Talk to Wizard of Xen in order to get to Smuggler Warehouse
b. Enter Smuggler Warehouse and then kill the first smuggler
c. I followed the steps made by mellowkat here in the forums to get hold of Guanidia and the hidden items
d. Afterwards, I hung out at the entrance stairs of Smuggler Warehouse and walked back and forth to engage in fights so i can level up
e. Spark levels up (level 30) and I allocate ST points.
f. Baretta levels up (level 30) and I allocate MN points.
g. Random levels up (level 35) and I allocate points .
h. Sarah levels up (level 32). I click Yes on the allocation message, but nothing occurs after.
I. I go back to Xen village and do the save.
After this when I level up any of the characters, i cannot allocate points any longer, and the allocation message somehow doesn't go away until I click on Yes. Not only that, I was able to see another strange behavior with allocating points in Smuggler Warehouse. For example, with Sarah, I was able to allocate long after the the bug occurred by clicking on "No" 12 or 15 times and then by clicking on Yes twice. Not sure why. By this time Sarah was already between levels 38-40. I have seen this happen for Baretta as well, I think, or maybe Spark - sorry I don't remember much about this anymore.
I currently play this game on my Windows XP virtual machine because i can't make 3 Stars of Destiny launch on my Win 7 64-bit. **edit: I installed the game on another one of my laptops (not on VM) and it worked fine, on full screen too. So this "can't launch" issue i had is moot.
I bought 3 Stars of Destiny on 8/5/2013 (2:32 AM Manila Time) and downloaded the installer on the same day from this site:
http://www.aldorlea.org/3starsofdestiny.phpI hope that you are going to be able to recreate the issue with the information above.
For now I will continue my adventures in Western Shores.

independence day is not for me; when i'm bound to you i feel so free... - bc