Pattern alignment

So I'm working on floor tile patterns with Illustrator. I love this program. The other day, I found (using the magical F1 key) that I can make a single 2-directional repeat of the pattern and make a swatch so I don't have to draw hundreds of rectangles. This is an enormous time saver and I'm very excited to have this feature.
My problem is this: I get everything done and ready to go, finish for the day, and save and close the file. I opened the file again today and found that all of the patterns are misaligned and out of place from where I want them to be.
Argh.  This happens whether I'm working with a PDF or an AI file.
Is there a way to lock the pattern position so that it doesn't get reset when I open the file? I've tried locking the layers as well as locking the objects, but still no luck with the patterns staying where I want them.
Thank you!
-Bennett

I imagine this would trump the advantage of smaller file size when using pattern swatches
In fact, expansion of Pattern Fills is one of the items Adobe lists in its knowledgebase as a means by which to reduce file size.
Pattern Fills are an old construct. Under the hood, the artwork being used for the pattern starts at the ruler origin and proceeds across the entire document. It is effectively masked (like a clipping path) by the paths to which it is applied. This is why, for example, FreeHand users who used alot of pattern fills in maps found it hugely advantageous to make composite paths out of any paths that shared the same pattern fill; otherwise, the whole pattern fill array was repeated.
A Pattern Fill is not the kind of newer construct like Symbols, where the artwork is stored in the file just once and then referenced for multiple positions.
It would be very helpful if the patterns would simply stay put.
Yes it would, and they certainly should. I am able to make a transformed pattern fill stay put between launches, depending on how/when/where the Transform Pattern Fills preference and/or the Transform Both command is toggled. But I was unable to boil it down to a reliable sequence. I suspect it's a ramification of yet another instance wherein Illustrator treats something that should clearly be document specific as a general pref--but I can't say that with confidence, because I can't get consistent and reliable results, and frankly lost interest. It smells like another one of those things one would have to keep a journal on to avoid tripping over it again later.
So if you're going to do this, go ahead and expand the pattern fill. There will still be more tiles than necesary, but the array will be confined to bounds of the masking path.
I do have a fuzzy recollection of a discussion in this forum years ago wherein Teri Petit explained the unwanted shifting behavior better. But I could not locate that, either.
JET

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