unclejemima,
No problem and I wouldn't expect you to be knowledgeable about all of this as I am sure your job isn't installing and supporting Mitel equipment so no worries.
The MiCollab Client is actually what was formally known as UCA (Unified Communications Advanced) and it had a desktop client version and a mobile client version both with a softphone add-on. It seems that you were only using the mobile version with the softphone and probably not the presence management portion; although it is still there.
As for Phone Manager it has the same two options of a desktop client and a mobile client both with a softphone add-on and obviously the presence management as well. The UCA and Phone Manager applications work completely differently, but they do the same things. So as you have probably figured out Mitel is throwing its support behind Phone Manager for the 5000/250 and MiCollab Client for all the other systems.
It sounds as though the application and possibly the phones settings are not properly setup on the phones you are using. The presence management portion can have a big effect on it as well. As to what the real problem is I couldn't say without looking at them myself. Your best bet is to get your vendor tech support or engineer to look at it for you to figure out what is wrong.
Personally, if the phone system is doing everything you need it to do for the remainder of your staff then I would look into getting the MiCollab swapped out to Phone Manager. Phone Manager has a lot of nice new features as of version 5.0, and it looks as though they are going to put a lot more into it. The product actually belongs to a company called Xarios, but Mitel has also had them take over a few other applications such as Customer Service Manager and I believe Oaisys Recording as well, and they are integrating them into the Phone Manager; the latter one I may be wrong about though. My company has just started supporting the product and from what I can see it is going to be a great product to enhance the 5000/250 for all of our customers; I personally like it better than the MiCollab server, but that is just me. At this point I believe my company is only going to sell the MiCollab to 5000/250 customers if they want the AWVC (Audio Web Video Conference) portion; which was originally designed by Inter-Tel who made the 5000/250. There is also the Mitel Border Gateway (MBG) that we use it for but we don't call it a MiCollab at that point even though it is the same server; semantics really.
Hopefully that answered your questions,
TE