Hi, Andy,
I have used the 50/1.4 as one of my favorite lenses for awhile now and I love it. But... wide open it is soft and has a kind of foggy, dreamy look. According to all the tests I have seen (with samples posted), this is typical. It sounds like you may be experiencing the same thing. But once you stop down to f/2 or smaller, it is crisp and clean and snappy... a wonderful lens. The same is true with the 50/1.8, except it does not get as sharp as the 1.4 until about f/5.6.
I use a Hoya Super HMC Pro1 Digital UV(0) filter mounted all the time. I have never had a problem that I could attribute to the filter, although I've certainly created some myself!
I've also discovered that the f/1.4 DOF is so shallow that it is very difficult to work with. Hard to get good auto-focus and hard to frame until you work with it for awhile. I nearly always get better results around f/2 or 2.2 and smaller. It took me awhile to learn this. Hope your learning curve is shorter and shallower. But stick with the 50. It is a wonderful lens!
Hope this helps.
God bless.
Doug