you couldnt give some advice on using winmerge again could you?

when trying to merge 139b files with 139c files winmerge is highlighting both panes yellow. Indicating that winmerge finds both files completely different.

but only on about 50% of the files i compare.

example admin/layout_controller.php shows 3 lines that have changed.

but admin/categories.php the whole thing is highlighted....

its driving me mad... as i have added mods that insert code to these files so i need to winmerge rather than copy the files over.

been at it all day, really ****ed off with winmerge
close to not upgrading 139b to 139c as i dont do downloads, sell music, offer free shipping, only use SWGUYs invoice as payment. had no session errors etc..

why does winmerge show the differences on some files and other says the whole thing is different?.. when i can see its not, its like 2 line different..

ARGH lol