I can understand your frustation, although both registries can give grief when it comes to paperwork! 9 out fo 10 it's pefect, but if something goes wrong . . .
From the breeding perspective, I personally want double registered, DNA/PQ breeding stock. AMHA's system for registration, may not be perfect yet, and may not guarantee parantage (with unscrupulous people) - but it's a start. I'm not purposely breeding for the pet market, as pets are born from the best stock, and we'll all get them occasionally from any breeding program.
My personal feeling is if someone is willing to market their horses for anything above a pet price, everything should be done - registration, DNA/PQ testing, etc. Those are things I'm looking for in the future. AMHR's paperwork with fill in the blank color - well - it's not good enough in my book. Photo ID and DNA helps keep most people honest - not perfect as the cheats will cheat!
So, last year was my last time to buy anything that is registered in only one registry. I have four that will be registered into AMHR ($1400) and one that needs to go into AMHA ($600+ dna test too). The cost is one thing, but unless a horse is an absolute steal, not again - the paperwork is just time consuming and an additional pain in the butt!
That said, we show primarily AMHR as we can show our tiny ones up to the B size. Plus here in California the A shows are much more expensive and less friendly. We show for the enjoyment not for the stress!
Marnie, you will never please every buyer, and you really need think of who or what you want to market too. If minis are under 34" (to me) double registered opens up a larger market. If it's causing you stress - don't do it! You can sell only AMHR, with an application to AMHA for the foals (assuming the parents are A's). There are plenty of people that specialize in only one registry with great success.
This is suppose to be enjoyable, if it isn't re-evaluate what your doing and make changes!