NIOS I EDS 12.1 and 14.1 unstable

Hi I'm experiencing unstaility of the NIOS II EDS IDE 12.1 and 14.1

When using this IDE I have problems everyday with includes that are randomly there but links are lost. We need to do index rebuilt and /or restarting the IDE and/or restarting windows 7 64 bits. It's even worse with 14.1.

Another problem that make us lost at least 2 weeks is application stop button...when pressing STOP button we are looking for that effect but as soon as we click somewhere else the program restarts (at least on the UART) but not on JTAG UART. The program was flooding the RS-232 port and make the other end freeze (Microchip PIC24F behind a transceiver) with random. We found that with the oscilloscope. Am I the only one having this issue?

Thanks