Sen2cor help and confirmation?

I have installed snap and sen2cor. When I confirm installation of sen2cor with L2A_Process -help I receive no errors. There are 2 issues I have been having when I try to run the tool in Snap.
1st, I go through the steps to install the tool into Snap, but after restarting Snap the tool disappears from the manage external tool and clicking on the sen2cor tool bar extension does nothing.
2nd, If I uninstall and then reinstall sen2cor under plugins than do not restart after installation the tool is there. But, when I go to run the tool I get the Warning: it seems there was an error on execution or the defined tool output error pattern was found. Please consult the SNAP log file. When I do that first thing it says is :
"WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/snap/s2tbx/modules/org-esa-s2tbx-s2tbx-commons.jar!/org/esa/snap/ui/layer.xml "
There is a whole page of other stuff as well.

 3rd, to get around this I have been able to run the sen2cor through the command prompt, but am unsure if it is fully working or not.  A folder is created with files inside, but the deal runs for awhile but then at about 66.5% percent process it  jumps to 100% : application terminate with at least one error.

Did this run completely or was there an issue? I am unable to open individual bands from the new L2A folder in snap and get an error while reading file message. I am however able to open the bands in ENVI and am able to note a difference in pixel values, but am unsure if it was done correctly. There is no visible difference between L1C and L2A.