Connection and calibration problem of waters LC/mass 2695/ZQ micromass 2000

Hi
I thank you in advance for patience reading the whole story
I have a lc/mass 2695/zq micromass 2000. First I have been told that signals are showing without applying voltage to the probe. But when I checked the device myself I noticed that isolation valve was in close position that was the reason of high noise without decreasing even after hours. 
After that I saw signals below 200 m/z without infusing any sample to the mass directly or via the hplc. So I cleaned the source, ion block and support, injection ports (whole rotor and stator) even quadropole to get rid of these pullotions. The intensities of these m/z s was in order of e6 but after first cleaning decreased to e5 (small victory).
In the next level, I thought that autotune and calibration may solve my issue of these unwanted mass peaks. Autotuning with 50/50 %v/v mixture of acetaminophen/caffeine (each 50 ppm) for tuning the various sections voltages failed. After that  I started calibration with NaCsI solution for static, scan and compensation types only static was passed and the other two failed.
In the next step I decided to define a new project to do all levels from beginning. After the definition I didn't see any signals in the signal windows unfortunately. And when I press acquire and try to scan m/z s but the software closes or gives this error "application phoenix UI has encountered an unrecoverable problem and has had to exit ..."
I must say that after this auto tune, calibration and new project definition the software stucked. It didn't change the ion mode normally and problems like this. Next I found the previous projects and uploaded them in the project list, the stucking stopped but the acquiring again ends in the Phoenix error. I think maybe the .ref file, acquire file that the project gets it's setting from has been changed and that is the cause of the problem because I wasn't familiar before with project definition maybe I didn't do something in the process.
I would be very grateful for any assistance
Sincerely yours
Bashir Majidi