Reply to Firmware upgrade complete but still got problems

Hi everyone

I am new on here so please be paitent with me.
Today i successfully (as far as i can tell) upgraded my vci100 to the new firmware (1.3) no boot fail messages ect. i have also added the SE overlay for traktor pro and upgraded to traktor pro.

I a having a few issues. when i go into the controller manager within traktor it is recognising the vci as a device but its not in the drop down menu for the "in port" and "out port" (to the right of the device) thus i am unable to cue correctly
Also when on the main screen according to the new overlay on the vci the sync button seems to stop the track as well as matching the BPM. i understand you can/should only sync to the master channel but when the new tune becomes the master you can not take sync off without stopping the deck.
i am also having a few issues with some of the other controlls (mainly fx and performance modes), it seems like its bcome a cross of the original vci and one with the new settings.

Can anyone tell me if i have upgraded the firmware correctly or is this a TSI issue?

any help much appreciated