It’s common within the Enterprise to run the services (or daemon processes if you prefer) under a special “service account”. This account is often a domain account that has very special privileges and as such no one is generally expected to use it for anything other than running processes that are part of The System. Sometimes you might need to elevate to that account to diagnose a permissions problem, but those occasions should be very rare.
What you want to avoid doing is logging on interactively to a Windows machine using that account, such as remotely via MSTSC. What you should do is logon with your own credentials, or better yet those of a “break glass account” and then elevate yourself using, say, the RUNAS tool. This allows you to open a separate command prompt, or run another process under a separate set of credentials - usually the service account, e.g.
C:\> runas /user:chris@domain cmd.exe
There are various switches to control the loading of the user profile, etc. but that is the basic form. Once you have the command prompt or process open you can do your thing in a limited kind of sandbox.
The first reason for not logging in interactively is that by default Terminal Services will only let you have 2 connections open. Given that some developer’s (and admins) have a habit of leaving themselves logged in for extended periods, you invariably have to hunt down who has the connections open and ask one of them to drop out. If one or other user is logged in interactively using the service account it becomes a much harder job of finding out who “owns” that session and, as we’ll see, just toasting their session can be dangerous.
The main problem I’ve come across with logging in is down to the way scheduled tasks that are configured to run using separate credentials (in this case the service account) end up running in the interactive session (even without the “interactive” box checked). If you’ve ever had seemingly random console windows popping up whilst you’re logged i, this could be what they are. If you’re lucky the keyboard focus won’t be stolen, but if it is or you’re clicking with the mouse at the wrong time you can block the I/O to the process by accidentally enabling Quick Edit mode. Or worse yet you hit the close box as it pops into life.
You might notice those effects, but the more deadly one is logging off. If one of these scheduled tasks is running at the time you logoff, it will be killed. You might not notice it at first (especially if it gets scheduled again soon after) but the scheduled task will have a failed status and the very curious error code of 0xC000013A (application terminated by Ctrl+C).
The second issue I’ve seen relates to the service account not picking up changes in Windows AD group membership. I’ve read various chapters from Keith Brown’s excellent book Programming Windows Security (which is admittedly getting a bit long in the tooth) but can’t see why this would happen. Basically the account was removed from an AD group, and then later reinstated. However at the time the account was re-added to the group there was an interactive session on just one machine in the farm.
The other machines in the environment picked up the change, but the one with the interactive session didn’t. I could understand that an existing process might cache the group membership, but even starting new command prompts didn’t help. The scheduled tasks that were running, which were also new processes each time didn’t pick the change up either. After logging the session off and logging straight back on again everything was fine.
Maybe it was a one off, or perhaps it’s a known problem. Either way my Google Fu was clearly letting me down - that and the fact that the key words to describe the problem are about as vague as you can get in IT (group, windows, cache, etc). Hopefully some kind soul will leave a comment one day which explains my experience and brings me closure.
 I’m sure there are some edge cases to that advice, but I can’t personally remember a time when I needed to actually logon to a machine with a service account. Well, I can, but that’s because the software used to hide the passwords forced me to do it when all I needed was an elevated command prompt. That aside I haven’t.