You're confusing remote desktop for administration with remote desktop services. Remote desktop for administration is for remotely managing a server via RDP. Remote Desktop Services is for remotely working from a server session as if the remote session were your workstation and running applications within that session via RDP. The conceptual aspects may be blurry but the licensing is certainly perfectly clear. In addition, remote desktop for administration is limited to 2 concurrent sessions and no additional licensing is required. Remote Desktop Services requires RDS CAL's and is limited to the number of RDS CAL's that you've purchased (this isn't a technical limitation, it's a licensing/legal limitation).
They may seem like the same thing and from a technical perspective they are (except for the concurrent session differences) but from a legal and licensing perspective they are two wholly independent things.
If you're running applications on the server while using remote desktop for administration you're most likely in violation of the EULA of both the server and the application.
Honestly, I don't know for 100% certain, but based on experience with SBS08...
Event 91: Something to do with the Activity Directory Cert Service not
being able to connect to the Active Directory. However after looking
at the Microsoft tech support site this apparently is not really an
issue as it is caused by the order services start in.
I suspect it really is an issue. All those services on the same box sometimes start in non-dependency order, and the cert warnings... well. Remote desktop, your SBS site, etc., all use those certificates. For whatever reason, your AD services are taking longer to start than usual, and your Cert service comes up before them.
(Also, if your SBS server takes over 30 minutes to shut down, well, that's also a service dependency thing. Exchange tries to contact AD when shutting down, but AD shuts down first. But I digress.)
To test that, try restarting the cert services, followed by all the misbehaving services (terminal services, etc.), and see if that helps.
My first recommendation would be to put up a backup domain controller. Not only would that prevent the cert service coming up before AD, but it's also a good practice from a recovery standpoint.
Barring that, you might want to look at the order services start in and consider whether or not you want to tamper with that.
Best Answer
Small Business Server (since 2003 I believe) supports Remote Web Workplace: basically a Web-based authentication front-end to allow users to authenticate on the domain and herd them to their desktops for Remote Desktop sessions or a Terminal Server.
Ties it all up nicely into an Outlook Web Access, file sharing (new with SBS 2011), and SharePoint portal as well. Have the 2011 version installed at about four clients at this point. Can't beat it for a server OS for a small business (say < 75 users).
The users would not be Remote Desktop'ing into the server though; it doesn't work like a Terminal Server in that sense.