I've done this flight in similar conditions 3x and found that the clearance given by NorCal catches the controller off guard who is working the area, or he/she doesn't like it.
The first time I was given: Livermore One departure, ALTAM, SJC direct, climb and maintain 4,000'. This was not what I filed after ALTAM including the altitude which was filed at 6,000'. The Liv One Departure is runway heading to 1,200' then right turn to 020, intercept the 060 radial off OAK to ALTAM intersection.
When I reached ALTAM it was a a RT turn to 174 I seem to recall to SJC. About mid way through the turn the controller challenged me on it. He was annoyed and told me to read back my clearance verbatim. When I did he said "That isn't going to work. Advise when ready to copy amended clearance." He took me up to 6K' and vectored me around. He seemed to be irritated throughout.
2nd time same thing happened except before turning at ALTAM I queried the controller. Again, climb to 6K' and vectors to basically what I had filed.
3rd time which you saw here was the same, with the exception of 6K' was in my clearance. Long before ALTAM ATC began giving vectors. It was much better.
Why this is happening I don't know, but I was ready to question before making another the turn at ALTAM even though my clearance called for it.
I should call the facility and ask what's going on with this. I'm sure there is a good reason, but I'm relatively new at this and have no idea what it is. I do know that NorCal controllers are very good at what they do. I find they are helpful when I call with a question as well.