Convert CR2 canon 5D files to Tiff in cap 20 pro

Having real problems when converting CR2'S files into Tiffs. 

The CR2'S look fine when viewed in Cap 1 20 pro but when I process them in capture 1 the files become corrupted, the files have many colour lines in them and the file is way of the color balanced raw files. Just a mess.

Has anyone come across this issues.

Any ideas how I can correct this

Many thanks

Andy