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Best answer (Chosen by asker)
This is also very common. The main cause of this is the source file itself! If it is an AVI file you can attempt to fix it by raising the priority of DirectShow Multimedia File Reader! This is dont by clicking option - environmental setting. Click the VFAPI plug-in tab. You will see DirectShow in the list usually with a priority of -1. Right click on the NAME (not the priority) and click higher priority until the priority is 2 and it is at the top of the list. Hopefully that will solve the problem!
If it doesnt, then another possibility is to frameserve from VirtualDUB to TMPGEnc! I wont go into this right here as a guide for it is already on the forum somewhere.
And another option, as a last resort is to select the area before you get this error message and encode that part, then encode after it and use merge & cut to make 1 file. You could do this by clicking setting, click the advanced tab. In the list you will see source range so select it and if it doesnt pop up, double click source range. You can then select before it and click ok! Then encode that part, go back later and select after itto ewncode the second part. Then, you click file - mpeg tools. Click the merge and cut tab, to join them!