You can run multiple versions of CVI on the same machine, including CVI 6.0. The main thing to remember is to install each version to an entirely different directory than the others. There will be only one version of the run-time engine installed though, and it must be the version compatible with the latest version of CVI you have installed (this is most likely already true on most systems unless it was explicitly removed and reinstalled apart from any IDE).
As far as NI-DAQ 4.9 (is this the version that you actually meant?), it should be usable in either version of CVI (5 or 6) when accessing the functions via the NI-DAQ dll. Now, the Easy/IO for daq function library you may have installed with CVI 6.0 (possibly even 5.0) might not be compatible with NI-DAQ
4.9. What you can do to remedy this is to copy the easyio.lfp and easyio.lib files that are installed with NI-DAQ 4.9 to each of your CVI versions' ...cvi\bin directories and the easyio.h file to your ...cvi\include directories (You may need to just install NI-DAQ 4.9 to a separate machine to obtain a copy of this version of the aforementioned files). Lastly, I'm not really sure why you are using NI-DAQ 4.9 (if you are), but I would suggest upgrading to the latest version, NI-DAQ 6.9.1. The upgrade might help you avoid any problems altogether.
Other than this speculation I will need further elaboration to pinpoint the problem.
Jason F.
Applications Engineer
National Instruments
www.ni.com/ask
