In your machine group settings try setting the option for avast to load after other system services.
Also, if you have cloud services enabled (reputation services in particular) and some of the machines are unable to reach, or slow in reaching the mothership, you can experience slowdowns. Network conditions may vary for two machines cut from the same image.
Also... If you uninstall avast, then look at what remains in the two folders you are removing manually? I bet it is some of the log files (how big is your avastnet.log file??) and other things in the ProgramData folder... Inspect what is leftover for abnormally large or small files, corrupt or truncated .dat files, url.db file, etc... One of those is probably the cause, or at least the mechanism of the problem, perhaps caused by an issue with the streaming updates, or etc...