onboard not shown in taskbar

Confirming. Showing Onboard in the taskbar was disabled some time back because of otherwise unfixable (at that time) issues in unity. That was a couple of months ago, though, things may have changed again. I'll see what can be done.

Should be fixed in the 0.97 branch now. Onboard shows up in the taskbar if status icon and floating icon are disabled. This is only enabled for Metacity though, I still can't get this to work reliably with auto-show in Compiz and Mutter.

You can find Onboard 0.97.1, that contains the fix to this problem in our Stable PPA for oneiric, precise and quantal:
https://launchpad.net/~onboard/+archive/stable

This bug was fixed in the package onboard - 0.97.1-0ubuntu1

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onboard (0.97.1-0ubuntu1) quantal; urgency=low

  * Request for sponsorship: New bugfix release available (LP: #999185)
  * debian/control:
    - add moustetweaks (>= 3.3.90) to recommends
    - update standards-version 3.9.3
    - remove wnck dependency from depends
  * debian/patches: remove fix_encoding_mismatch.patch and update series
  * Improve auto-show:
    - unhide for combo boxes (helps in qtoctave) and date editors
    - add focused attribute to debug output
    - fix iconifying by title bar button
    - fix bad repositioning the very first time onboard pops up
    - fix non-critical backtraces for auto-show
    - fix keyboard not being hidden on startup in Metacity
  * Detect running environment to better care for its specificities
    - fix and make also window type hints environment specific
  * Add command line option to override automatic environment detection
  * Fix Onboard not being shown in taskbar (LP: #990486)
  * Prevent zombie process when launching preferences (LP: #936332)
  * Only appear in gnome-screen-saver if onboard was running (LP: #938302)
  * Don't check for running Onboard if "Typing Assistant" is on (LP: #938302)
  * Fix potential encoding mismatches in exception handlers (LP #958385)
  * Fix idle transparency kicking in while typing into firefox awesomebar
  * Change spelling of the unity property to ONSCREEN_KEYBOARD
  * Properly set up WM_CLASS to be above dash (LP: 915250, LP: #931331)
  * Switch window property to type XA_CARDINAL for compiz
  * Release all keys before quitting Onboard (LP #978430)
  * Simplify opacity transitions to fix some transparency glitches
  * Stop blocking the unity launcher icon for some seconds after each click
  * Skip transition delays on screens without compositing
  * Suppress python error messages when stdin or stderr are lost
  * Fix glitches when toggling force-to-top mode or decoration
  * Don't flash the icon palette in lightdm
  * Don't create the icon palette when embedding
  * Improve robustness of showing/hiding the icon palette on startup
  * Keep keyboard and icon palette above unity-2d dash
  * Don't get resized by compiz grid plugin
  * Try to honor rotating screens in gnome-shell
  * Use deiconify for metacity when minimized by titlebar
  * Remove wnck dependency as gtk3's window-state-event reports iconification
  * Don't save window position for maximized or iconified windows
  * Stop endless loop of auto-showing and hiding hiding onboard in dash
  * Fix visibility of active modifier keys in scanning mode
  * Make sure to remove the maximize button on recreating the keyboard window
  * Don't try to hide keyboard when turning on force-to-top while iconified
  * Switch all translated strings to unicode (LP: #933030)
  * Improve robustness against errors in translations (LP: 968044)
  * Import translations from the Ubuntu Translators team as of 6th May 2012
  * Fix geometries not being saved when exiting from the very first launch
  * Briefly present the keyboard when unhiding
  * Add middle click in hover click mode; requires mousetweaks >= 3.3.90
  * Make improvements in Onboard's...

Updated to ubuntu 13.10, and this problem came back. Installed version is 0.99.0-0ubuntu1.

Yes, confirmed, the "GNOME Flashback" session uses compiz now. The fix was only for metacity. You can get the old behavior back when you start Onboard like this:
$ onboard -q metacity

I'm not sure yet if we can makes this more permanent. In the short time I tested, I couldn't get the keyboard to become stuck invisible anymore, but there is still the animation delay for minimizing/restoring. Also, in order to be visible in the task-bar, force-top-top must be disabled, which triggers new bug #1242625, where the keyboard resizes every time it shows up. I have no workaround for this.

If you'd like to help, try running Onboard like above for some days and report back on your experiences. If there aren't any other issues, perhaps we can add a special quirks mode for only the GNOME Flashback session.