Not working; Previously created .QSYS file in a new project.

You should first solve the system ID problem. As long as this isn't fixed you shouldn't try to run the application.

Each time you re-generate the QSys sytem, new system ID and timestamp values are written in two places: in the generated HDL files, that are later compiled by Quartus, and in the .sopc info file that is read by Eclipse to generate the BSP. If you have a system ID problem here, it means that you have an inconstitency between what Eclipse thinks it should read, and what is actually returned by the FPGA.

It can be either because Eclipse is using an older version of the .sopc info file, because Quartus compiled the .sof file with an old version of the generated QSys system, or because the .sof image currently in the FPGA isn't the latest one. I also had license problems several times, and then Quartus generated the image in a different file, a _time_limited.sof. As I was still uploading the other .sof file into the FPGA I had an inconsistency.

Can Eclipse show you the expected timestamp and the actually read value? That way you could at least show which one is the more recent.