If you patched the correct ROM, it should work.
My guess is, that you either have used an unheadered ROM or the wrong version. Refer to the backup of the original ROM you have downloaded and look at the file size (Right-click -> Properties). If it says 2,097,152 bytes, the ROM is unheadered and most likely not suitable for patching. You can use HeAdder
in order to add a header in this case. If it still doesn't work, refer to this
thread. Hit Ctrl+F in order to search for "Which Yoshi's Island ROM version do I need?", it's all explained there.
You can also send me the IPS file you are trying to patch and I can tell you more about it.
--------------------NEW! SMW2 Yoshi's Island
Last update: 2012-12-31