As soon as the FLX extensions were changed to DWG, the routine then attempted to look for each of the symbols in the location specified in the AutoMAP library.  Being most of those locations are now incorrect (it is still looking in the old MSCAD2004 folder locations), you will get a message telling you that at least 1 block was not found.

If you were to look in the command line, you may see a whole range of symbols not found, due to the paths being incorrect. Example below:

The AutoMap library is still looking in the original path to find the DWG symbols (although it is now looking for DWG rather than FLX files).

To correct this problem you need to edit the AutoMAP library and change the path from the old location to the new location where MSCAD2005 stores the symbols.