Is "quirky" always a compliment?

Good question. I think you will find it depends very much on the sociocultural context. I note that eccentric/eccentricity can be substituted for quirky/quirkiness throughout:

Translation is a profession, and, whether you like it or not, you will find that quirkiness is usually not seen as a good thing in an employee. If someone in an office is quirky with regard to their way of working, this certainly could be a polite way of saying that they are difficult to work with, or that they do not follow standard procedures.

When it comes to the very top of professions, quirkiness may be valued (e.g. Steve Jobs might be called quirky), but this sadly is a luxury that most of us don't have.

However, if you have a circle of friends who are interested in music, art, literature and so on, then quirky may well be a compliment. If you've ever seen Friends, Phoebe is a prototypical quirky friend, and she is of course well-liked.

Edit: And of course it may depend on the culture at a higher level. For example, somebody with a quirky way of working might be tolerated in a London office more than in a Beijing office. We know that some cultures encourage conformity more than others. (See The Xenophobe's Guide to the Chinese for an entertaining discussion; it's not actually xenophobic!)