I was running into what may be the same issue that rivers88 was reporting. I had enabled auto-mapping for most of the NI complete plugins, but the wrapped plugins were only showing up for some of them.  For instance, I could see the wrapped versions of Massive and FM8, but not the wrapped version of Absynth. (I could see all items in Studio One, so this appeared to be a strictly Cakewalk issue).
 
I decided to investigate and found that the wrapped and unwrapped versions of absynth were both in HKEY_CURRENT_USER\Software\Cakewalk Music Software\SONAR\Cakewalk VST X64\Inventory, but that the 
CLSID for the wrapped Absynth was the same as the unwrapped version. Further, the CLSIDs for the plug-ins where the wrapped version does appear in plugin manager were definitely different from their unwrapped counter parts.
 
That led to the following KB note:
https://www.cakewalk.com/Support/Knowledge-Base/2007013293/Missing-Plug-ins-ProChannel-modules-resulting-from-8-3-Short-Name-file-optimizat
 
They have instructions for how to check your system. I was also able to use the following (on Windows 8.1):
PS C:\Program Files\Cakewalk\Shared Utilities\Internal\Overloud> FSUTIL.EXE 8dot3name query D:
The volume state is: 1 (8dot3 name creation is disabled).
The registry state is: 2 (Per volume setting - the default).
Based on the above two settings, 8dot3 name creation is disabled on D:
 
I then performed the following command (which you do completely at your own risk):
PS C:\Program Files\Cakewalk\Shared Utilities\Internal\Overloud> FSUTIL.EXE 8dot3name set D: 0
Successfully enabled 8dot3name generation on D:
 
I then:

• disabled/enabled the Absynth wrapper in Automap (This re-creates the file with an 8.3 name)
• reset my scan inventory from plugin manager (so it will create a new CLSID)
• re-scanned my plugins
• verified that a distinct CLSID was now created for the wrapped version of the plugin
• was able to manage the Automap wrapped version of Absynth, insert it into a project, and control it from automap

The KB instructions talk about moving your plugin directory to the desktop and then copying it back, that will create the 8.3 names in one fell swoop.
 
Heh-I just realized that all of the plugins where I could see the wrapped version had short names (e.g. FM8, Massive). The real name of Absynth is "Absynth 5". I wonder if when they generate the CLSID, they are taking the 8 characters of the 8.3 name, and if 8.3 isn't there, taking the first 8 characters of the full file name.
 
At any rate, I hope this helps someone.
 
 
 
 
 

I realize this is an older thread, but thought that with the Automap 4.10 release (supposedly "supports SONAR") there might be more experience base. 
 
I just upgraded to SONAR Platinum to take advantage of the <forever...> thing, and at the same time, have bought a Novation SL Mkii 49 for my DAW (been using my NORD for a long time, but it does not have a pitch wheel, which I miss more and more (I have even twice dragged my Roland XP10 out of the attic recently, but it is 'sad'). 
 
I'm liking Platinum and getting used to some of the recent layout/workflow update/changes. I followed the instructions to install Automap. Bottom line...everything works, but with some annoying stuff. Some of the learning pain was not knowing what to expect in terms of workflows. I thought that I could list the annoying things here and see if I'm missing an opportunity to make it better. 
 
1. The mixer seems to work great, although in my search for synths, I failed to notice that there is no <Master Volume> slider on this synth. A mile dissatisfier, but I'll live...my trusty Frontier Tranzport has a volume knob.
 
2. Automap did create wrapped files for all the VSTs and RTASs that I pointed it to...these show up in the directories with the same file name with < (Automap)> appended...yes, a space and 2 parentheses in the file name. However, inside of SONAR all the menus just show two entries with the exact same name. My first thought was...OK, I'll just figure out if the AM one is the top or bottom entry...turns out to be random. So my workflow to insert a synth or effect becomes: try one of the FX/Synth entries, then open it up and see if the automation information comes through...if not, then try the other one. 
 
3. This brings me to the next issue. The first time I open a wrapped synth (or FX) the SL Mkii flashes and comes alive with all the controls. Subsequent closing and opening does not work. Sometimes it works if I push the mixer button on the SL and then open the synth, sometimes it works better if I push the Instrument button on the SL. Haven't been able to figure out a systematic approach. 
 
4. Needless to say, this uncertainty is a drag on workflow and productivity during the formative stages of a project, which is where I hoped I would get the most from this controller. I read the "8.3" comments above and mostly understood, but it seems to be a different problem...please comment or correct me if I'm wrong. It would be great to get some type of Automap label in the SONAR listings to distinguish the two. Maybe I have to just use the editor to hide all the non-automap files??
 
5. Is there anyway to reverse the wrapping process and start over, other than manually going through and deleting all the files with Automap in the label?
 
...this was more of an adventure than I hoped for, however, overall I like this synth a lot. Normally, I don't like synth keyboards, but since I have the Rhodes and NORD on tap, I opted to get something with fast repeat capability...it is a very responsive keyboard (a little touch at higher velocities, but I'll get used to it). I like the Roland style Pitch/Mod lever as well...it's mucho improvement over my XP10. 
 
Please comment away if you have anything to add...4.10 seems very close, but shared experiences can certainly help. 

Sorry for taking such a long time to reply, but there's a couple of things that might help:
 
If you go to Automap window, you can select which plug-ins you want to wrap. Clearing the enabled check box will delete the ... (Automap) plugin. Rechecking it will recreate it.
 
In Sonar, click "Plugins" and then select "Manage Layouts". All of the registered plugins are shown. As each registered plugin is selected in the center list, the name of its DLL is shown at the bottom of the window. Create a layout that has the Automapped plugins and you're good to go.