Maybe you can provide some more info on how exactly you've set this up. When I create a mask path and apply the generate>stroke effect to it and then animate the start and end properties I do not have this problem. By the looks of how your stroke is changing width along the path I suspect you might not be using the stroke effect but something else.
Hmm...I'm not sure how else to explain it. I made 2 paths 1 for the "L" and one for the rest of the signature. On both I applied the "stroke" effect and animated the start or end to get my effect. Whenever the path overlaps on part of the signature, it blocks the piece its supposed to show (see image). I'm not sure how to correct this since the direction given on the help guide seems to apply only to older versions of AE possibly.
OK so...after racking my brains about how you were getting such clean variable widths on a simple stroke effect I've deduced (without any help from you) that what are doing is drawing paths over the original text & trying to use a stroke effect to reveal it. What part of "EXACTLY how have set this up" did you not understand? Don't just assume people know what you're doing, especially considering you don't even know what you're doing.
Try disabling AEs default composition background (which you no doubt have set to white). This background is fake...it does not render and is kind of stupid feature that cause more confusion than anything else. Always use solids to create backgrounds.
When you disable the backround you might find that what you though was happening is not what's happening at all.
Let's start there.
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Your technique is not good. You should be using the animated stroke as a track matte. You should not be trying to match the background color with the stroke. That's never going to work.
You'll also have to add additional mattes to fix the overlaps. It is actually easier in most cases to use the paint tools and write on to simulate hand writing.
If you have a little while to wait I have a tutorial that is almost done showing the most efficient way to do this kind of animation. It may be ready tomorrow morning. If it is I'll post it. For now take a look at this screenshot. It shows how the animated masks work to fix the overlap problem.
Each of the masks fix an overlap problem. As the write on effect reaches the mask mask opacity is animated off so the whole letter is revealed. Here's more of the timeline revealed. The t is just starting be be drawn and you can see that the tail of the i sticking up.
This is by far the easiest and most efficient way to simulate hand writing when you have overlapping lines. You can use Write On, or an animated stroke effect using a mask path or a path from a shape layer with the trim path shape animator added. All will reveal the text when used as a track matte but all of the techniques require that you have some animated masks to fix the overlapping lines.
I meant zero offense in that reply. When I said "I'm not sure how else to explain it" it was because I actually wasn't. There was no snark/condescension implied by my response. Thank you for your input on resolving the issue.