Reality Filter just gives +1 to initiative if you win the test. The -1 to all rolls would have been because of improper protocols. In other words, you wouldn't get a bonus to everything if you succeed, just a penalty if you fail. The bonus is inherent from the fact that all the programs you're up against are outdated and won't be able to put up much of a fight.
As to hacking, I'm running this very differently. This system is so old that its firewalls are essentially made of paper. It hasn't been updated in 20 years, so any vulnerabilities they would have had back in 2050 would be comical security lapses in 2070. The hack is assumed. (Also, I really hate how the new matrix is just a bunch of extended tests. Roll a bunch of dice is not fun to me. Out thinking and out-maneuvering the system seems cooler.)
However, as this is an executive level computer system, every node you come to will be running IC, some just to monitor users and lock down the system if it detects you, and some of it will be black as it gets, though it's not going to have the kind of ratings that you'd expect.
System + Response 4d6.hits(5) → [4,6,3,2] = (1) So, your filter manages to make sense of the old system.
Analyze tells you that this machine is running a basic Access piece of IC. It will scan for activity each turn that you're in the system, and set off an alert if you can't verify your account privileges. (that means it will try to beat your stealth, and if it can't then you can do whatever you like on the system for a whole CT worth of actions, so 3 passes, and if it does, you can try and spoof it using an ID you find on the system records.)
Anyway, it scans you. 4d6.hits(5) → [6,5,4,4] = (2)
Roll Hacking + Stealth +2(hotsim) to match or beat 2.