Your ovaries don't strictly alternate between one and the other each month. Especially not if you're using follicle stimulating hormones to support your IUI. FSH (eg Puregon) can actually produce mature follicles on both sides at the same time.
The only way to know which ovary is going to produce the lead follicle in any given month is to undergo monitoring via internal ultrasound. If you're using Puregon with your treatment, then this is meant to be started on day 4 of your cycle. If you've missed that, have a word to your FS about how to proceed.
And as an aside: have you had a laparoscopy to determine the state of your tubes? Sometimes an FS will recommend you go straight to IVF if the health of your tubes is in doubt. I think this is good advice - nobody wants to go through an ectopic.
That being said, I have a friend who fell pregnant naturally on one tube. So did Nicole Kidman! Nature can be very mysterious.
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