I cannot allocate any skill points to my Character or BO's.
Actually, I can allocate the points, but the button to accept the changes has been replaced with the text "Skills Invalid" next to the Respec button.
If I allocate points and then try to remove them, I get a message about setting the skill below it's minimum and it pops up a window which would normally have a list of the affected abilities, but it is blank. This only happens with any skill, but only to the first skill I allocate points for. If I add points to other skills, I can adjust them as one normally would be able to before committing the changes with the accept button.
I first noticed the problem after reaching Lv20. This is my second Fed character, started after I purchased the CE Box on Amazon. I had previously purchased the Enterprise Bundle from the C-store, and used my NX Ship From Lv1 up to Lv20 playing Elite difficulty. I didn't even bother picking a Lt. Cdr. ship, electing to use my NX as a challenge to myself, until I could use my Thunderchild Escort at Lv20. Also to challenge myself, I had not allocated any skill points since Lv10 or so.
Also, Once I reached Lv20, I did not receive a Cdr. ship voucher.
This issue came to exist from the November 1, 2012 patch. You can read about the cause under the General section in the patch notes.
There is an existing thread discussing this issue, and you can read it here for more information.
Personally, the "free" respec worked for the toons I tried it on, but not everyone has had the same experience.
On November 1, flyingtarg from Cryptic posted that they are working on the problem, but there has not been an official update since.
Try the following steps (if you haven't already):
1) Open up the toon Skill UI and click on the "Respec" button
2) Confirm that your toon's skill selections have all been reset to 0.
3) Close the toon Skill UI
4) Open the toon Skill UI and check if the "Respec" button is now changed to the "Accept" button
5a) If so, allocate your skill points as normal
5b) If not, file a ticket and/or post about it and/or wait until the problem is announced as fixed
Regarding the Commander Ship Token, what have you tried to confirm that you did not receive it? Assuming you accepted and completed the "Promotion Commander" mission for your toon, when you talk to Lt. Laurel on the second floor of ESD, you should be able to filter the ship selection to Commander level ships. From the results, there should be three ships that can be purchased with the cost of 1 Token. If you do not see the cost as 1 Token, what do you see instead?