I appologize if this is a repost of any kind, but I can't seem to find any answers and so far I've gotten no answers from STO/Perfect World:
I spent 500 Zen on February 23, 2013 to alter my Skills in order to increase my shields. When I was learning the game, my goal was to get all Skills to a yellow marker and move on, but I found out later that by maxing out certain ones, I could increase my Shields even more. I paid the 500 Zen at Earth Space Dock, edited my new settings, chose Apply and OK. I went back on Monday, February 25 to take a screen shot for another player to show them what I did, but all my Skills are back to yellow marks. The settings I applied are no longer there, but the Zen I spent to change them were deducted from my account.
I was informed by GM-Unception that I needed to submit a Bug Report instead of going through standard troubleshooting support. It has now been three weeks since this issue has been submitted, and I am no closer to a resolution than when I submitted the original ticket. I was not specifically informed how to do so, however ("With that said, we would like to encourage you to submit a Bug Report, with your findings, directly to our QA team. This may be done by selecting 'Bug Report' from the list of available help options."). I looked all over the website and finally did a search to find out I had to submit this in game.
I was also informed by a few other players in my fleet that there is a known bug with altering your skills: If you do not reset ALL skills, any action you make to change them will be reset to their original settings. Again, I have heard this from different players. Unfortunately, I am still 500 less Zen with no updated Skill settings.
Submitting a bug report in game does not give you any kind of ticket number, nor is there any way to check the progress of the report, or if anyone even received it. I find it very frustrating when spending real money and getting no results.
Have you opened the respec window to see if you sill have a respec token? Yes this is a bug and you need to choose the Clear All option and redistribute all of your skill points. This will also, thankfully, reset all of your Romlan and Omega reputation passive abilities and you will need to rechoose them. You won't loose any XP or progress in the rep system, just need to repick your abilities. Kinda nice though for people like me who chose the wrong abilities and wanted to change it.
I respeced a character a couple weeks ago because I made changes to his build and needed to rechoose my rep passives. Worked fine for me when choosing to clear everything first.