The behavior you describe is working as intended. Check the Season 7 Release Notes, under the "Systems" section. Third bullet down in that section explains what you saw.
Anything you donate to a Starbase project is gone... forever. That's how Starbase donations have worked when Season 6/Starbases were introduced, and Season 7 does not change this.
What you get to keep are the Fleet Credits you got for making those donations.
The "stuck" "Contribute" button is a bug. If you had x officers donated prior to to Season 7 release, and the new requirement is less than (or equal to?) x, the game does not change the "Contribute" button to the "Filled" button. Clicking the "Contribute" button does bring up the officer selection UI, but if you select any officers and hit the "Ok" button, no officers will be donated to the project. However, if you fill in all of the other requirements for the project, the game will start the project. (I personally tested this.) Therefore, the "Contribute" button bug does not affect gameplay, at least in my case.
I finished off the required fleet marks for one of the missions with the 'stuck contribute button'. It did in fact start the project like snovern said it would.
As for the stuff being gone once committed, that sucks! You would at least think since that part of the mission was complete it would have stayed complete. Especially since it went from purple to white doffs.
Last edited by milkmanmhoc; 11-14-2012 at 11:58 AM.