To make NetBeans start as optimized as possible the boostrap code as well as all installation technologies (installer, autoupdate, native packages) need to cooperate with each other.
The communication is based on one important file: .lastModified present in each cluster. More info:
It has come to my attention that RPMs for 6.8 are not generating this file. This makes it almost impossible to distribute updates of RPMs: without such files the application classes are going to be read from userdir caches completely ignoring any changes in cluster JAR files (just observed during my work on bug 185342).
To fix the problem please modify the RPMs to always touch or create .lastModified file with recent timestamp when a content of a cluster is modified.
Victor said he is targeting to fix in in 6.9 packages.
Indeed, it is already implemented in the 6.9 packages, but they are not published yet. I'll close this bug when the packages will be published.
FYI this bug is also tracked on the wiki page with overall status of the packaging of the NB 6.9:
Packages are published, so closing the bug