Endpoint Protection

I am currently running SEP11 and when I try to do manual scans on select clients, the scan will not be received.  The users are online and this does not seem to help?  Any idea what could be the cause of this problem?

Which communication mode did you set up for your clients? If you are in PULL mode with high heartbeat value, such scan command may take time to reach the client (i.e. you're in PULL mode with 2 hours heartbeat interval, so client may receive this command from 1 to 120 minutes after you send it). In PULL mode, clients are dealing with client/server communication, and sending commands to them won't break/reset heartbeat counter (the only way to do so is to right-click > Update policy locally on the client). 

To check it, go to Clients > YourGroupOfClient > Policies tab > Communication settings and check the mode (PUSH/PULL) and heartbeat value.

You can also see if the command has been successfully send to clients in real-time in SEPM console (Monitors > Commands). What do you find there?

It is set in Push mode with a 5 minute heartbeat interval

Try by rebooting a client system

If you launched the scan from the SEPM console's client view (as I suppose): Did you check the command status (Monitor > Command Status tab)?

"You can also see if the command has been successfully send to clients in real-time in SEPM console (Monitors > Commands). What do you find there?"

Did you check this?