1.) Nowhere in my global settings is 'view only mode' checked, however I've noticed the 'view only' option turned on when sometimes connecting to VNC servers. I've done some further investigating with this and realized that it only happens when you connect to a server that was already there when you opened VNCM, to replicate this problem
We had no luck reproducing this problem. The same is going to item 4). Also two customers using the VNC Manager to manage their large corporate networks were asked to try to reproduce both bug reports and none of them could reproduce the bug. 
2.) When using SC UltraVNC File Copy, VNCM is almost non responsive and VERY slow when working with other VNC sessions or the main VNCM window. Other sessions are incredibly slow, even when on a fast link (this is not a bandwidth issue). Using two standalone UltraVNC viewers works fine, so the problem lies with the SmartCode branded versions.
This is something new. This will be investigated this week. Does it matter if there is one large file or many smaller files being transferred? Also what’s CPU usage% the task manager showing during the transfer?
3.) When using SC UltraVNC File Copy trying to copy whole folders, SC UVNC FC ignores folders. So if you click on a folder on the local PC, then click copy, it quickly flashes and says 'Transfer Complete', but nothing is copied. This is the same if you're copying the contents of a folder which includes files and several subfolders, it will copy the files but NOT the subfolders. This is definitely an issue just with the SC versions, using the standalone UltraVNC viewer this is not a problem.
Same as 2) will check on it this week.
5.) The VNCM registry editor cannot import a Windows Registry v5.0 .reg file, it gives the error 'Invalid registry file format'.
The bug has been fixed. Thanks!
2.) Ability to automatically scan DSF folders on program start (currently only able to scan Registered computer folders)
This sounds like a useful addition. Most probably it will be implemented in the v4.0 release.
3.) Ability to scan ALL DSF folders at once (would be advantageous when you have 50+ folders like I do)
I guess Stop All Scans command would be useful also. This will be implemented for sure.
4.) Ability for the 'update logged on user' function to only scan computers that respond to ping requests. The function is VERY slow if it tries on a computers that is offline, MUCH slower than a 500ms ping timeout.
This is a good idea. It has been implemented in the v4.0.5.0
5.) Alternative method for retrieving MAC Addresses (sendARP doesn't resolve outside local subnet)
We have done some research regarding this issue. Nbstat.exe uses "Netbios over TCP/IP" in order to fetch MAC address from a remote computer.
The problem is that by default "Netbios over TCP/IP" is disabled. But anyway, we might consider adding this method as an option, so a user could choose, which query method to use.