> Sometimes the files would be merged immediately and sometimes I would get the dialog box to merge
When using the context menu, the user intent is clear. It is easy to understand what you want to merge, so the dialog seems unnecessary. Using the toolbar feels more like the user went out of their way to use the toolbar. Why? Maybe to select additional files or to provide a file name?
I can see where it's a little weird, but I think the different behavior is justified. The alternative is to probably show the dialog when using the context menu as then behaviour is consistent. That takes more steps, but it has the advantage of being more consistent.
> In the resulting dialog boxes for those tools have a clear indication as to what file is being acted upon
That's a great point. I will review this before the next release. Thanks for highlighting this!
> disabling (greying out) those buttons when multiple files are selected
This is a good idea. We had reasons why it is implemented as it is, but I can see how the current implentation could cause confusion for new users. I will take a closer look and see if there is an easy solution. If not, it might be better to improve how we indicate which file has focus. This might help users understand the target of the toolbar actions.
> don't allow multiple files to be selected if the majority of buttons/commands only act upon one file
This is how LogViewPlus worked for years. We had feedback from users asking for multi-select to make it easier to merge files, etc - and I think the feature makes sense. It's hard to please everyone.

Thanks again! I will take a look and post back here when a BETA release is available.
Toby