Ok. To clarify, it seems that although Section Access supports >1M rows there is a limitation that reduction field(s) in in the Section Access table cannot handle more than 1M unique values. This is where a setup like rubenmarin suggests above comes into play.
I've got a temp fix in place for now to limit the table to less than 1M unique values and will work on the clean solution in a couple weeks and post the results here.
Do not know if you have seen the following info, but this might help. You can also leave a post on the blog posts and Henric will likely reply. I know there is a 2 billion unique data point limitation as per the QlikView Reference Manual in the Appendices, but I am not aware of a Section Access limit, so this could be a defect, and if you are a licensed user, I would suggest you open a support case with us, so we can look into this. There are some other blog posts here as well that may be helpful to you in understanding things at a deeper level and rather than me trying to find them all, I will let you look at them yourself to determine which ones may help in addition to the ones below:
Primary Design Blog link:
Section Access/Data Reduction links:
I hope this might help, sorry I do not have exact info regarding the limitation you appear to have hit.