As its seems the new version of DOSbox (0.74) isn't recognized. If I manually pick the install folder of my DOSbox version it just says that my version is too old or not found and doesn't let me proceed - and that sucks.
Any ideas?

Talk to GOG support. If DOSBox somehow changed the way they indicate the version number, then GOG will need to correct their installers.
In the mean time, you could just install the game normally, and then manually point it towards your existing DOSBox installation.

That's what I'm talking about. It doesnt even work manually. Sending a mail to the support...

Ah, sorry. I thought you meant during installation. Still, the game works with the built-in DOSBox version, no?

Ye, indeed. Still, it would be nice to have fixed installers so enjoying the games with the updated version is easier.

True. Well, it's good that you notified GOG of the problem. They'll need to deal with it anyway the next time they release a DOS game, and get the latest version of DOSBox for the installer. They might as well deal with it now.

I have sent the mail.
Can anyone confirm this problem?

Which game are you talking about? They don't all use the same launching method. Some of them call a DOSBox installation directly, others use gogwrap.exe.
And how are you trying to point the game at the other DOSBox installation?

Well, I have tried Masters of Magic and Masters of Orion till now. Testing a few more....
And as I said: I'm just talking about the installers for now, not launching the games with the new version.
Same for Duke Nukem 3D (although I would use eDuke32 anyway ;) ), Earthwom Jim 1 & 2 and The Settlers 2 Gold . Check the attached screenshot.

I notice you are running both the game and dosbox in program files, have you right clicked the gog installer and selected run as administrator before trying to install?

So you DID mean during installation after all. Have you tried installing it normally and then changing it afterwards? I know I asked this before, but I think we both misunderstood each other.

You could try installing dosbox outside program files folder (say c:\dosbox\) then try to install the game outside program files as well (c:\gog.com\). This way you don't have to constantly fiddle with administrator settings when installing old games.
I finally got money so I'll buy and try master of magic later today with my laptop (win7 premium 64-bit) to see if there's problem. I'll do the same with my xp pro desktop as well to see if it's vista/win7/64-bit thing.
Edit: actually if it works with my lappy when I test it it may be due to having disabled UAC... well see later today.

Those few times I've tried using an already installed DOSbox, I've met the same problem. I'm not terribly bothered by it though, I could just copy the DOSbox files over to the game's installation if I want to use the latest version. Of course, having a single install would simplify upgrades, but it's not that big a deal in my opinion.

Yeah, just dump them straight in, confirming replacement when prompted. The start menu shortcuts and everything else will work just like before as if nothing had happened.
Older GOG installers--including Duke Nukem 3D's--are hard-coded to look for 0.72 and only 0.72, and will not accept newer versions. Changing the install locations and messing with UAC and whatnot will not rectify this. I don't know whether GOG has corrected this for releases using 0.73 (I don't own any of those).