It seems that there is a case when Spark is not able to extract all plugins included in the installation, so some plugins are missing files and are not working. Maybe this was just a one time anomaly, will have to monitor. In my case Roar and Flashing plugin in my Spark profile only had "native" directory extracted, missing libs. Had to delete all the plugins in my Profile and let Spark extract them again.
Just hit another weird case. I have noticed that Roar popup is not being shown and a message is not visible when this is a first message for a new tab. Also Reversi and Tic Tac Toe icons were missing in the chat window. There were too many jars and folders in the plugins folder (like it extracted a few versions of the same plugin). After wiping out the plugins folder and letting Spark extract them a new, it went away. I think this might have happened when i have installed newer build on top of older (both 2.9.0).
This happens every time i update Spark to a newer build (installing same build on top doesn't have this effect). It seems that Spark checks if there was a newer version installed and tries to reload all plugins in user's profile on the first run. And fails to properly do this for plugins with native libraries.
After searching about this i think maybe we can use Delete files and directories to get rid of the flashing and roar directories in the user's profile during the installation. But the problem is that Spark might be installer with elevated user's permissions and the user running it can be different, so there will be no way to point to a user's profile during the installation. This has to happen on the first run of an updated application.
It appears that the install4j installer does not directly affect the installed directory. I'm assuming that it is Spark itself that deletes a plugin, and then re-installs it.
I've found that when deleting a plugin, Spark deletes all files in the plugin directory, plus a subdirectory named 'lib'. Is there a good reason why Spark does not simply remove all subdirectories (which then would include 'native')?
Looks ok now. After the update to 199 build it has updated all the folders and files in flashing and roar plugins' folders.