When you have multiple instances of shareplex when applying a 5.3 patch, it will touch all the vardirs available on the box.
There is a file called vardiirs.log in the bin directory. It has a entry for other vardirs available on the box.
For example you have 5.3. 0 and 5.1on your system. When you are applying 5.3.2 patch it will prompt you if you want to apply the patch to 5.1.
Delete the entry/entries of the vardirs you are not patching.
Then apply the patch.