I spent hours reading many posts on internet, some money ordering EEPROM as per those post' suggestions, some more hours trying to install various software from both Cypress and Salaee... all without success. Really, I don't recommend going this route unless you have a lot of time and very little money. If there are any problems, you will need a lot of advanced skills and time..
I guess you had a bad device, but I agree, it is not really a solution if you need something guaranteed to work every time. But hey, then you are probably not shopping in the $8-$10 department neither, are you?
BTW, motivated by @mavey's comment, I have just built Sigrok for my Logic clone and wow, that thing probably blows the original Saleae software (the stable version) out of water - both in terms of hw support (it supports even my Brymen meter, my Rigol scope and my OLS Sniffer, nice!) and protocol decoders available. Very very nice!

I still need to do some real testing on how well it performs, but so far it looks really promising.
If someone wants to give it a shot, I have followed these instructions:
http://marcusjenkins.com/linux/saleae-logic-analyser-clone-with-ubuntu/ It is not the easiest thing to build, because there are many dependencies and you need to be proficient with building software in Linux (automake/autoconf use and CMake use), but it compiled without issues.
As for Logic Sniffer, I agree the client looked rather disappointing. As a professional Java developer, I can say it was the right choice for multiplatform and any lack of features is certainly not the fault of language - probably a simple lack of time and interest from the developer.
I don't think that the main problem was Java neither, but the language choice caused some self-inflicted wounds, like the chore with getting serial ports working in Java using the RXTX library, which is absolutely horrendous in terms of reliability and bugs ... If you need to talk to hardware, Java likely isn't going to be the best language choice, because you will have to rely on JNI libraries to do so anyway. Then the only benefit of using Java is the "built-in" cross-platform GUI.
If you want to build multiplatform software, you certainly don't need Java for it, especially when the sw in question is open source and there is thus no problem with recompiling it. Even proprietary software can be easily multiplatform without relying on Java if well written - e.g. the original Saleae sw.