Hi there!
I had the same problem but managed to fix it.
Go to Printer Settings and try this:
1. make sure your baudrate specified in the Printer Settings matches the baudrate of your board's configuration (in my case a Mega2560 programmed with Arduino)
2. set "Reset on Connect" to "Disabled" instead of "DTR low->high->low"
3. click "Apply" and "OK" to store the settings and return to Repetier Host.
After this I was able to connect again to my printer and control it manually as before in version 095.
I hope it works for you as well.