There is a bugfix in v2.5 that fixed a problem with Optimize and high scale/density combinations causing random density variations. Unfortunately it turns out that some old parameter files with Optimize on and high density settings now have very different density balance. It is not possible to improve the existing density handling without breaking compatibility of some old files one way or another.
If you find an old file that doesn't appear as it should, or has densities out of balance, and Optimize is checked, try it with Optimize off, or set all holon densities to 1. If that is a big improvement, then see if some holons need some density adjustment.
For one example, if you open the Sample file "Dirk Monteny\20070313spiral03.xep" in v2.5 the spiral is invisible, but seting all holon densities to 1 fixes it.
If you find an old file that doesn't appear as it should, or has densities out of balance, and Optimize is checked, try it with Optimize off, or set all holon densities to 1. If that is a big improvement, then see if some holons need some density adjustment.
For one example, if you open the Sample file "Dirk Monteny\20070313spiral03.xep" in v2.5 the spiral is invisible, but seting all holon densities to 1 fixes it.