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 I just really don't know what's the reason... I mean as in your case my other lifts have been steadily going up (squat, military press, rows etc.) my bench is the only "problematic" exercise in terms of progression.

Yeah exactly. I really struggle with gaining strength while more or less in a constant caloric deficit. I recently tried out to cut down from 92kg (205lbs) to 86kg (190lbs) but after two weeks I just had to realize that my body just doesn't handle dieting and training hard 3-4 times a week. So basically right now I'm just trying to stay at around the same weight while improving my body composition. I think that way I can be at a lean 205lbs by the end of the year without the need of a real cutting phase. It worked pretty well so far. This last month I stayed at 204-205lbs morning weight while my waist measurements went down and all other measurements went up a bit. So his concept of recomposition is actually working for me.

Box squats (parallel) 150kg for 4 sets of 5. Benchpress 100kg x 6, wide grip pullups with 15kg additional weight for 8 reps.. strength is coming along nicely... now I just need to cut down some of that weight (90kg @ 1.83m). 

I highly recommend sliding leg curls or swiss ball leg curls to you... I'm currently doing lots of them and my hamstrings are definitely getting a lot stronger.. plus it's a really joint friendly exercise.

Here is a article by ben bruno about sliding leg curls describing some possible progression/variations.

http://www.t-nation.com/free_online_article/most_recent/hamstring_hell_sliding_leg_curls

Yeah.. same here. But at the moment I don't do BSSs. Both my legs are on the ground. I might incorporate some BSS back into my program at some point but I actually like this variation a lot more especially because balance is not so big of an issue. 

By the way my upperbody pressing strength is pretty pathetic at the moment. I did 45kg for 10 reps yesterday, whereas my 10 rep PR is something like 60-65kg. Oh well... it's far from a priority anymore though so I'm not really concerned.

I do them with a medium stance.

barbell... goal is 3 plates (140kg) for 10 reps... would be sick. 

About your shoulder issues: I don't know what exactly is bothering you but what worked wonders for me was doing lots of rowing type movements (cable rows, db rows whatever) and stuff like YTW's, band pullaparts, face pulls, dumbell protractions/retractions etc. for the upperback.