Printer asking about repairing permissions means there was some error, but nothing serious or suspicious?
Likely nothing serious. If you don't mind, I'm going to go on a bit of rant here about repair permissions (mostly in response to the rather alarmist post by Robert_James_The_Third). If you don't want to read all of this, just jump down to the last paragraph or two at the bottom of this post.
First, a quick aside: as a unix sysadmin with nearly 30 years of experience under my belt, it's *extremely* painful to read posts in Mac support forums about "repairing permissions". It's often treated as some sort of magical voodoo cure-all, or curse, depending on who is posting. File system permissions are nothing magical and it can be (and is) entirely normal for the permissions of a file to change over its lifetime.
Permissions being which user/group owns a file, and whether it's readable/writable/executable by the owner, group and every other account on the system.
A little history: Repair permissions was originally introduced in OS X back when OS X was in beta and most Mac users ran the *old* non-Unix MacOS operating system. If you had both OS X and Mac OS 9 installed (for dual-booting), it was possible that OS 9 (which did not have a concept of Unix-style file permissions) could inadvertently alter the permissions on some of the OS X files. So Apple built a repair permissions feature into Disk Utility and it has been there ever since.
The Repair Permissions feature in Disk Utility goes through the system files as well as any apps you may have installed one-by-one, and compares their current permissions with a record of the permissions set when the app was originally installed. If there's a difference, Disk Utility changes the permissions back to the original setting.
The trick is though, that there may be good reasons for permissions to change - e.g.: when you first install an app it may have one set of permissions (owner: you, group: staff, readable, writeable, executable). But after you run the app for the first time it may need to elevate its permissions. Or an update might come along and the new version of the app installs with slightly different permissions.
Now in the case of your printer driver, it looks to me like the developers used the phrase "repairing permissions" for a stage of the install which likely changes the driver file owner so that it's owned by the print server application on your Mac. Why it doesn't print properly is another question (some of the Gutenprint drivers are flaky - such is the life of open source print drivers). And when you reinstalled it, the installer was likely smart enough to notice that the drivers you installed previously already had the correct permissions set, so it didn't need to "repair" them again.
So in closing: You almost certainly don't have a trojan. You likely have a poorly-written open-source printer driver problem. And when it comes to repairing permissions, remember: unless you're dual-booting OS X and OS 9 (on a PowerPC Mac!), 99.9% of the time it's voodoo.
Now: Which printer and version of OS X are you trying to get to work together? Maybe we can help.
