For Tmpgenc you require the Vfapi plugin for Avi Vfw compatibility. Then Tmpgenc should have no problem reading your Avi file. If you already have the plugin installed then I guess some software has changed the plugin settings so go to the plugin settings in Tmpgenc and reset it to recommended settings(see the help).
As far as Vdub goes, choose full proccessing for both audio and video(select some good codec - i prefer divxv4.0 - see the help file and guides here for good quality settings) in the settings and select "Append as avi" for the 2nd file and 3rd file and select save as. You should get a new avi with the codec and settings you selected in vdub. If this has been done then(did not work) install the latest version of Vdub after installing the previous version(delete).
Hope this helps.