smooth edits without re-encoding - failed with virtualdub

Tried to get smooth edits with fades without re-encoding the entire video using the following:

• Cut the required portions in Virtualdub by choosing start - end points on keyframes and choosing Direct Stream Copy mode.
• Made avisynth files for the portions where fades are required
• Used Virtualdub to encode the avisynth files to avi with the same bitrate settings
• Used Virtualdub "Append video segment" to add the files together and save the result using Direct Stream Copy mode.

Unfortunately, this does not work. The files got with Direct Stream copy and the freshly re-encoded fade bits don't work with each other, Virtualdub complains "The video streams do not share a common sampling rate" - it detects one frame rate as 30 and the other as 30.00003 fps.

Tried installing Adobe Premiere Pro CS2 - that also does not work without re-encoding (except for DV files etc.) "Smart encoding is a feature enabled in CS6."

Edit: 12 Feb - Tried Boilsoft Video Joiner  for joing the clips. Gives exactly the same error, so probably it uses vdub as the backend! But Avidemux succeeded in doing the job.