Well, for one thing, lime takes some time to work its magic. Your yellow onion variety may have been more forgiving than the red as far as acidity and the other factors that ph plays in nutrient uptake.
Generally i've found that my red onions are more prone to not sizing up when nutrients are lacking, especially Nitrogen.
I would take another ph test close to the time of planting to see how the lime is working, lay on the compost very heavily and watch the plants growth closely. If they seem checked you could side dress with the OG fertilizer or water with fish emulsion if needed.
Maybe others will chime in with some good ideas.
Cheers.

Thanks for your reply.

Hadn't considered the amendments still working in but it makes perfect sense. Another test this fall is also a good idea.

Any suggestions to lighten/loosen the soil other than the compost?

The lime will help loosen the clay as will the compost. Contrary to popular belief, onions don't really need loose soil to thrive, they're not carrots forming roots below the ground. They do however need good drainage as soggy soil causes all kinds of problems.
I'd focus on increasing organic matter and fertility. Also, try a few different varieties, some will take to your place better than others.

I should have asked already, are these overwintered or spring planted?

I agree some yellow onion varieties are more forgiving and much larger than the average red onion. You did not mention variety but it also possible that you have a variety not suited to your area.

Not sure of the varieties but they were started from seed at a friend's greenhouse this spring.

I do know the seed came from Fedco (Maine) who typically favors stuff for our climate, but they may have been a short-day variety. I'll have to find out.

Inspite of the clay, the drainage is good at that site.

Thanks for the insights

A technique I use is to "band" fertilizer beneath the plants before setting them out in spring. I make a deep furrow (6-8 inches) and place about 3 inches of compost mixed with a blended organic fertilizer, mix this with some soil, and set out plants on top of the buried cache of nutrients. The nutrients become available just when the plants hit their early summer growth spurt.

Variety makes a huge difference, too. I love the long red topedo onions for fresh eating, as well as small red cippolinis, which keep really well. But for general storage onions, the yellows have the reds beat, IMHO.

You may want to check the variety, Fedco offers Red Bull and Red Wing which are large red onions, but they also offer Pearl size Red Marble and small size Rossa di Milano.