Mac app store problem: some applications that are not installed are seen as installed

After configuring the new imac, I open the mac app store, and although I have not installed any application of previously purchased, I see them as installed. I can not download them again.
I tried to delete one from the old imac, but nothing changes.
Tips?

Andrea, it is still difficoult for me to understand.
In your first post you wrote "After configuring the new iMac", later you write about a backup disc, an old Mac etc...
Configuring the new iMac: I imagine you got it with an OS installed and you imported your stuff from the old Mac with Setup Assistan (Assistente Installazione) or Migration Assistant or from a Time Machine backup. The difference between Setup and Migration assitant is explained here https://discussions.apple.com/message/19130045#19130045
Or did you simply copied your Apps and data from one mac to the other ?
Sorry if this question may be seen stupid or offending: I only try to understand.
At the end of the Migration you should have disconnected the external disc (or the other Mac in Target mode). Why then you opened the AppStore ? I imagine to download again some Apps which were not transfered by the Migration process. But since you write you opened the AppStore AFTER the configuring I assume you did it from the new iMac booted from its own disc with other drives disconnected. Or do you have a copy of the old system on the same disc ?
About the question of "open with" you write that sometimes the files ask to be opened with Apps in the other disc instead with the same App on the boot disc. You have to disconnect the external discs and again use the Open with command but select "Other", find the correct App and chack the box "Open always with this App" (Apri sempre con questa applicazione".
If you have some Apps not yet migrated from the old system to the new one I do not understand why, because Migration assistant should transfer all Apps (Apple and third party). Should it be possible to do a second Migration ?

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