With SolidWorks 2007 and prior, most commands are available through on-screen toolbars. These toolbars are highly adjustable, both in content and placement. Sometimes, their adjustability in placement can cause issues that may make it seem as though SolidWorks isn’t saving toolbar placements. In my experience, SolidWorks does a good job at saving placements of toolbars. The issue many have with saving toolbar placement is often related to the fact that SolidWorks allows the same toolbars to be placed in different locations for each document type (drawing, model and model assembly).
It should be noted that some people do experience a real problem with toolbar placements not being saved. This problem is caused by a corrupt install or registry. To correct this issue, use regedit.exe to rename/delete the SW registry key (HKEY_CURRENT_USER\Software\Solidworks). This allows SolidWorks to establish a new registry key, and hopefully eliminate the corrupt information. (Note: this will clear all Solidworks settings, so use this method with caution.)
But, before that method is attempted, try this less drastic method first. As stated above, sometimes the issue is caused because different document types are using the same toolbar, but that toolbar is in different locations for each. This causes them move around when switching between document types. As they move around, they push other toolbars around too. Each time this happens, they can cause toolbars to shift into even more different locations. The solution is to have a drawing, model and assembly all open at the same time, then switch back and forth between them to see what jumps around. Adjust locations of the toolbars with each document type active. Switch back and forth from that document type to the other types. Do this for each of the three document types. Keep doing this until all toolbar locations are stable, no matter which document type is open, and to which document type is switched.
Then here’s the most important part: exit SolidWorks normally. It is the exiting of SolidWorks that saves the toolbar placements. The process can take about 5 to 30 minutes.
A side note, if SolidWorks crashes at any time after toolbars are changed, but before exiting normally, any changes to the toolbars will be lost! This is important to note, it is it a third reason why toolbar changes aren’t saved.