It sounds like you have two apps that both are trying to be the default handler for the same file type(s) and they do not have identical coverage of the available mechanisms exposed by the OS. Furthermore, the install/uninstall of an application has further muddled the settings, possible because it did not properly clean-up after itself during uninstall. You will have to clean these up to reconcile the discrepancies.
Open the Control Panel, then the Default Programs interface, and you should see several options to manipulate the associations between file types and applications.
1) Set your default programs
2) Associate a file type or protocol with a program
3) Change AutoPlay settings
4) Set program access and computer defaults
Set Your Default Programs
For your scenario, I think you might want to start with #1: "Set your default programs". It will take a minute to compile the list of applications, and then display those applications on the left. Select the application that you want to be in control (i.e. when you double click or right-click->Edit) so that it is highlighted. You should now see some information about that application. Assume that you have Paint .NET selected.
Notice the statement "This program has X out of N defaults" (where X and N are numbers). You can briefly switch to the "other" application, say Windows Paint, and take notice of the same statement- "This program has X out of N defaults" (where X and N are numbers).
I think you are saying that you would like one application, say Paint .NET to be the main application for handling PNG files for all verbs. Make sure Paint .NET is selected and then choose the option "Set this program as default". That will assign all of the actions to this application and consequently un-assign any other competing applications.
Associate a File Type or Protocol with a Specific Program
If you still aren't getting the behavior that you desire then you might need to look through the associations defined under item #2 to refine the action that you desire.
Change AutoPlay Settings
This shouldn't really come into play for the scenario you describe, but I just want to share with you my personal preference when it comes to the configuration for this type of functionality. I turn AutoPlay off. I have two reasons that I prefer it that way. First, for security. The AutoPlay functionality has been a key mechanism leverage by criminals trying to install malware onto your system. By turning it off, that attack vector is severely limited. You would, and could, still install an attackers malware if you explicitly ran it, but I suggest you don't do that.
Second, it prevents OS chugging/churning from an application trying to start-up in the background when you trigger one of the AutoPlay hooks. Instead, when you are ready navigate and initiate the application that AutoPlay would have started, but do it manually. This way it starts when you are ready, not as you are trying to finsih something before switching tasks and having AutoPlay interfere with you ability to quickly complete the task at hand to move on.