Happy to help here. I would try the following:
Create an intermediate metric (let's call it Score by Employee):
SELECT MIN( SCORE ) BY ID ALL IN ALL OTHER DIMENSIONS
Then, once you have this metric defined you should be able to create a metric for the average score as follows:
SELECT AVG( Score by Employee )
The reason we create the first metric is to force the table to normalize score around the ID attribute which gets rid of duplicates when we use this in the next metric (we could have used MAX or AVG also, it doesn't matter). Hopefully this solves your issue, let me know if it doesn't work and I'll be happy to help out more. Also feel free to check out GoodData's Developer Portal for more information about reporting:
https://developer.gooddata.com/docs/reporting
Best,
JT