yep, yards (and professional marine work in general) are like that. they quote an outrageous number (if at all, some just say "time and money"), do a job that is decent at best and downright shoddy quite often, and then bill you significantly more than originally estimated.
this is why I try to do almost everything myself (except when I don't have time, tools or expertise).
On the upside I asked my yard to do a few small jobs on my boat about 3 weeks ago. Well, they are presumably done as of yesterday (though I haven't seen the results yet) and the charge is $500. There was no estimate (they work for time and materials) but this is only about a $100 more than I thought it may cost (and right on with the amount I thought they would bill for the job). 3 weeks to do something is a HUGE improvement over most other yards I dealt with (where nothing would EVER be done for months without constantly reminding them). Now if they didn't screw things up too much - I will consider them a perfect place.
They did fix something on my boat last year in about 3 days and I was on the way, so this would be a second decent experience. Not to jinx it - I'll report on results this coming weekend.