When you changed the pads and bled the brakes, did you change from DOT4 fluid to DOT5 fluid? I seem to recall that they are not compatible, and the rubber master cylinder seal may have become affected in some way, leading to a sudden failure (although I may be wrong on this).
I have heard this also. I was also told that they react with each other and form a sort of gel!
If the system is still tight and your fluid levels are still OK as you said, then it's a really difficult one and I'm struggling to come up with an answer, mainly due to limited knowledge.
I've also noticed a slight weeping of fluid from the bleed nipples on the calipers. I had the same problem on my GSXR1000 which also used Nissin calipers. I cured that on the GSXR by wrapping the bleed nipple thread with PTFE tape before putting them back in. That sorted that problem, however I doubt that was the cause of this problem.
All I can come up with is a problem I had on on my 1996 ZX-7R when I used it on track. After a few sessions the lever would be coming back to the bar. I tried everything: different pads, different brake fluid, braided hoses, bleed brakes with fresh fluid before a track day. Nothing worked. They were Tockico calipers and I came to the conclusion they just got too hot and boiled the fluid.
What I would suggest, possibly backed up by you saying the brakes never felt as good after fitting the different pads is that possibly you haven't got all the air out the system and the fluid is boiling up and compounded by the air in the system you eventually reach a point where they are too hot.
Before working on them, what are they like now you haven't used the bike for a while?
Other than that if no fluid is leaking out, maybe there is an issue with the MC as you suggest.
Like the others, I really hope you solve this one. Keep us posted.