I downloaded my raw DNA data from Ancestry and uploaded it to FTDNA for free. I later paid for some extra features, such as being able to use the chromosome browser. I wouldn't say I have had problems with it exactly, but when it says you have an "X match", you do have to look on the chromosome browser to see how big the matching segment is as some of them are very small and not significant. Also, when they find a DNA match over whatever their minimum is, they then add all other matching segments, however tiny, to the total, so their figure for matching cM's tends to be over-inflated.
But I haven't had any male relative do the Y-DNA test on there. I think it is generally agreed to be the site where you get that test, though. I haven't heard of other people having problems with it.
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