after some further thought and observation, I think I have found the problem:
The situation only seems to occur with nations that start the game with core national claims either on colonies, or other nations. What happens is that when nation X gets control over those provinces, and makes them states, there is an initial surge of assimiliation, that disregards POP size. Going back to the USA and Oregon, when I make Oregon a state, the vast majority of those Polish Catholic POPs will become Yankee Protestants. Now, as this reduces the size of those POPs, the remiander get quickly assimilated, having been reduced to around 15% of their levels prior to statehood.
Now, this is only part of the problem. The next factor is that national culture POPs (yankee in the USA), grow at too fast a rate. Again using the US as an example, by 1900, in the GC, I generally have 200,000,000+ over all population. This is about 2x where it should be. This population boom does not result from immigration as it should, but is instead the rapid growth of domestic POPs. Because of this growth rate, immigrant POPs are just over whelmed, and get assimilated so fast as to be a non-factor.
third is how immigration/emmigartion is working. The way POPs move about seems to be quirky at best. As most foreign POPs will only move in numbers less than 500, they tend to get assimilated faster than they can arrive to build up the POPs. Also because of this, cultural minorities in places like Austria tend to get nickle and dimed to death (150 Czechs move out of Prague, get assimilated, process repeats until the original POPs are gone). It's also why the Ottomans tend to be too stable in late game situations. All those ethnic minorities are severely reduced by then.
Lastly, is the type of POPs that immigrate. while aristocrats should not tend to emmigarte (except to national colonies), the lack of Clergy immigrants also speeds up the rate of assimilation in foreign lands. Clergy tend not to be assimilated at all that I have seen (same for aristocrats and capitalists), but they provide a factor to the general state of the immigrant POPs (as can be found through the ledger page for POPs). Now, while I have seen clergy move about, it's in very small numbers (under 100), and they seem to like only warm provinces (Hawaii, Carribean, Oceania). You won't find any moving to Alaska, or Tibet, even if the other numbers are very enticeing for immigration.
So what's to be done? 1. Slow the rate of growth for national culture POPs. the over all growth rate is too high for the GC, especially among the great powers, as they tend to have all the growth rate bonus techs and inventions. 2. Increase the size of immigrant POPs. They need to double if not triple in size. 3. Increase the tendency of clergy to immigrate. Again, the size needs to be increased. also, Clergy POPs tend not to grow at all (go figure-

), so the numbers of Clergy world wide rarely fluctuate during the game. Some sort of growth potential needs to be there.
Now, is there any way, under the current 1.03 version, that this sort of thing can be done with out changes being needed to the hard code?