When I compare schemas from 2 instances, all my code objects are listed as
different. Show Difference Details tells me that there is one extra blank line
just before the final '/' in the code objects of one instance.
The only difference I can think of is that instance is characterset AL32UTF8,
and the other is WE8MSWIN1252. No such problem for two instances with
WE8MSWIN1252. (The first instance was "converted" from the second.)

Very tedious to inspect all those code objects individually. (Oddly, no such
problem comparing single code objects, only when using compare schemas.)

Here's a suggestion that might help with this, and might also be pretty useful
generally.

In "File Comparison Rules"/"Define Minor", add an option to "ignore blank
lines".

Oh yeah, I'm using Toad 9.6.1.1 and instances are all Oracle 10g.