AICS2 flattening causes massive color shifts in nontransparent objects

Seems like I should find this here, but searching for "flatten" didn't do the trick. And I apologize for not knowing the answer to such a simple question. It's just never come up for me before!
I have several files all created the same way that and PDFs from them will not print properly on the color inkjet system my local Staples is using. They're asking me to flatten the files before creating a PDF. (Perhaps another vendor might work, but I think I should know how to properly flatten my files in Illustrator.) Here's the setup...
A bottom layer contains a bunch of embedded PNGs to create a map. Over that, different layers have text and stroked paths. Some of the layers are made transparent (in different percentages). Some are not transparent. My Document Color Mode is RGB, all my colors are RGB and my PNGs are RGB. Seems relatively simple. Now here's my problem...
Even though my first test PDF looks right on screen, it printed improperly: all transparent objects were more or less ignored by the color printer. (All opaque text knocked out very well.) So they suggested I flatten my file in Illustrator, then export a PDF. I've been trying to do the flattening and can't get it to work. No matter what settings I apply the bottom layer of PNGs gets "ghosted:" it shows up looking like it's been reduced to about 30% "transparency" or tint.
As a test, I made a new layer and put a simple color rectangle on it. I turned off the PNGs layer, and tried to flatten. The color rectangle was also ghosted. In one case (can't remember exactly what setting were being applied), PARTS of the rectangle were ghosted, and other parts remained the solid color. (I've also seen the same effect applied to the PNGs: parts of them are ghosted, parts not.)
I have tried pretty much every combination of options I can think of in the Object > Flatten Transparency dialog box. I have tried setting the transparency Appearance of the layers to Multiply instead of normal. I have tried applying transparency to the objects themselves, instead of to their layers. Nothing will prevent AICS2 from ghosting (tinting, call it what you will) the color rectangle or the PNGs, even though they have no transparency applied to them.
Obviously I have no idea how to proceed. I've used transparency effects in Illustrator (love'em) before, and have had no problems with printing from InDesign. But Staples needs a PDF.
And oddly, if I export a JPEG, all the transparency effects have been applied perfectly correctly. Perhaps that will be my final workaround, but for learning purposes I'd like to get this "flattening in Illustrator" business at least somewhat working. Any advice will be appreciated. I'm going crazy!

Thanks for lending a hand. Mordy's article seems to me to deal mostly with recovering transparency after making an EPS. So I'm not sure what it has to do with flattening within a supposedly original AICS2 document. The article and its comments do mention flattening when printing, as does your post #4, Wade.
Are you telling me I can't successfully flatten the relevant layers within my document, and have them stay that way? I'm not printing these files. I might be able to ask Staples (or any other print shop) to print them in a special way, but that really seems kind of clumsy.
I tried a test. Following what I think Wade meant for me to do, I used the AICS2 print dialog, with the settings as in post 4, and saved as a PDF instead of actually printing. I then printed that PDF and the problem PDF on my Brother laser printer, and noticed several differences. The old PDF didn't have some of the transparent elements on it. The new one did have them. So I'm hoping that "Printing to PDF" may have solved the immediate problems.
If the only way I can successfully flatten these files is when "Printing to PDF," what's the use of having a Flatten command in the Object menu? Am I still missing something? It would be very helpful to be able to flatten the layers that need flattening, and leave them that way. (They are static. I'm finished those layers. They aren't going to change any more.) Then I could work on other layers in the meantime and just do a regular old "Save as PDF" when needed.
Anyhow, it's great to know I might be able, with your kind help, to have these files print correctly!

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