On Mac OS X, the bug below still exists. In short: when in simulation you select the variables to view, this selection is not remembered between simulations. So when fixing a bug and returning to the simulation, you'll have to re-select the few out of many variables you want to see.
+++ This bug was initially created as a clone of Bug #69 +++
Unlike the View->Processes... menu item that remember which processes has been
deselected, the View->Variables... does not.
You are simulating a system with lots of variables. You decide to deselect half
of them. If afterwards want to deselect a single extra variable, you have to
again deselect all the variables you deselected the first time.
I just checked under Linux. At least with fischer_symmetry.xml, it doesn't work either. Will investigate further.
Fixed in the 4.0 branch from rev. 3064.
Clarification to original bug report: This bug is not the same as bug 69. Bug 69 was about the dialog box not recovering the previous selection. Bug 409 is about the selection not surviving a reload of the model into the simulator.