Happens for me too - very annoying. I used to have 5 workspaces in a row under Ubuntu 10.04.
However, I did find that putting 4 workspaces in 2 rows stops the windows from jumping around. It's harder to click on a workspace but that's my fix for now.
There doesn't seem to much motivation to implement some EWMH support in Firefox nor in Chrome, even though this would get the restoration to workspace issue resolved with a large number of desktops. A bug has been open for Firefox since 2007 and one for Chrome since 2009.
What you can do outside of Firefox and Chrome, if the active TABs in different browser windows point to different URLs, is to use tendency that different URLs usually have different titles associated with the pages and hence with the window in which they are displayed.
Starting with that idea you can use the output of wmctrl -l -G -p which provides you with
- window id
- workspace number
- process id
- x,y position of window
- width and height of window
- machine name
- window title (if any)
for each window. Given a process id PID you can see where the link /proc/PID/exe points to and filter out non-browser windows. For the browser related windows, save at least the window title and workspace number (possible also the browser type and all the other information).
After a browser (re-)start, when all the windows are restored, but on in one workspace, use the saved data to lookup the new window id, WID, associated with a specific title and push it to the retrieved related workspace with wmctrl -i -r WID -t workspacenumber.
If you don't want to implement the above yourself (it is mostly text processing and a symlink lookup) in your shell or scripting language of choice, you can download a program that does all this for you (and a bit more). Or you can install it from PyPI using:
sudo pip install ruamel.bws
after which the bws command should be available with options to save (multiple saves are kept, 10 by default), list (show the saved dates with number of windows saved), or restore (by default the latest saved info).
Best Answer
I've just realized that it happens only if I have Google Hangouts conversations opened. They are on every screen and after workspace switch they are focused instead of last window, even if minimized.
The solution is to go to Google Hangouts' Chrome extension settings and uncheck the "Keep Hangouts on top of other windows" option.