Check the glyph order. I remember I had the same issue. When an alternative form of a glyph precedes the basic form, some applications used the alternative form automatically. The improvement of glyph order (basic glyphs first, alternative then) solved this.

About glyph order, yes, I had this too once.
About aalt -- actually FLS does not add an aalt feature when generating fonts. An aalt feature is added when importing a font back into FLS. You could use ttx or any other tool and search for "aalt" to find it's not there unless you added one manually before generating the font ...

No I never added it. So maybe it's not there. There is no default substitution. After all it's default. My font order is Windows Code page. The alternates are way down at the bottom of the font. The defaults are not mentioned in the Open Type features at all really.

What exactly the problem is swash glyphs are being used instead of the default glyph. Now I use Calt to apply the swashes and it works flawlessly in Adobe's
programs like expected.

Now that might not even be the problem. There might not be anything wrong with my font period but it seems from what I'm hearing is that the calt rules are not being applied properly in some applications. What applications I don't know. Everything I've tested it in it works like it's suppose to. Could be Mac applications.

Some applications seem to be ignoring the substitution rules.

Calt is on by default in InDesign. You should use the "swsh" feature for your swashes and the "zero" feature for your slashed zeros as these should be turned on manually. Calt means contextual alternatives, and I would put perhaps a feature like this there:

sub g j' by j.calt

where the j.calt is a normal j but with a little smaller tail in order to be replaced ONLy when it meets a g on the left side.

That is the way I have it set up. It's a script font so there is beginning and ending swashes for words. There is even singles. It works as expected in every program I've tested it in. I also used swash but for more elaborate swashes.

I'm using Calts ' feature to pick apart the words so only the correct letters get subbed, I'm also using ignore subs. Like it's working like it's suppose to actually he did give me the name of the program with the problem. Hang on I'll go find it.

He noticed the problem with this program:
OSX 10.5 using the TextEdit app

I never tested my font on a Mac. I don't have a Mac available to test it on. I never said my font would work on a Mac. It should but it's untested.

Ok, I think I misunderstood your problem, and still dont really understand it, I guess.

Is it working everywhere except in TextEdit on a Mac?
Is that the issue?

Processing of "calt" in Mac OS X 10.5 is broken.

Thank you Adam

"Processing of “calt” in Mac OS X 10.5 is broken."

That is exactly the answer I was looking for. I was sure that there is nothing wrong with my font. Like it works on everything I tested it on. Seemed kind of odd that there is a few programs out there that I didn't test it on that are having problems with it when the vast majority of the programs, Even High end programs are having no problem what so ever. I never made a system up to get my swashes working I used documented examples to make it work correctly.