I am experiencing the exact same problem. I tried firmware 0.9.4, which didn't work at all, then both 0.9.3 and 0.9.2 which both exhibited the same symptoms you describe: working at first, then corruption in the filesystem noted by non-printable characters in the root directory. I had some files in the /www/ directory which remained usable, and I could access the web interface, but over the course of 24 hours of it being powered, I lost the ability to ssh into the LinkIt, and when I did a hard reboot (MPU reset), it locked up during boot with the continuous orange WIFI LED lit.
I saw one or two comments elsewhere that this board might have issues with corruption during power cycles, which is unfortunate since that is inevitable in my application. However, my flash corruption seemed to occur and get worse while the board was powered and sitting idle.
I'm with you: wondering if there is an issue with the flash on some chips (mine was bought through Amazon on June 2nd, could look for lot code info if that is on the board anywhere), or if there is an inherent design issue with the flash getting corrupted.