When doing a schema comparison, it seemed that the extract of program scripts lacks a sort on argument position. Therefore randomly Toad get the arguments in a different order which results in a difference being noted that does not actually exist.
Eg. when comparing 2 scheduler programs (1 in each schema) that has 3 arguments that are identical and deployed with the same source. The first schema extracted the arguments in order of 2,3,1 while the second schema in order of 1,2,3 from the script.
Waiting for a fix in a future release of Toad for Oracle.