I'm seeing odd behavior (might be intentional) for the one-dot modules (first tier)...
Speed: Energy: +10%, Speed: (none), Quality: -1%
Efficiency: Energy: (none)
Productivity: Energy: (none), Speed: -20% Productivity: (none), Pollution: (none)
Pollution Cleaning: Pollution: (none)
Quality: Speed: -20%, Quality: +1%

Quality is the only one that looks right between Tier 1 and Tier 2. All the other Tier 1 modules appear to be missing their reason to exist.
Am I missing an update? I don't have much else (besides the Bob's Suite) loaded as mods. What data can I gather for you?

Sounds like something has gone strange with your mod settings. From the main Factorio menu, open mod settings and reset all Bob's Module settings back to default.

Duh, thanks for the hint. It appears that some of the values were changed. I don't recall doing that, but I did start the game a few weeks ago.

Never mind. Sorry about that. Feel free to delete my idiocy. 8)

All good. Glad to hear that it is sorted

Not stupid at all. The exact same thing happened to me. Just installed the game a week ago to start a new playthrough with a Vulcanus start. Started pumping out T1s and found they were only doing their negatives, no positives. The specific thing I noticed was the 'Speed Bonus Start' and similar settings were all set to 0. That makes me think the settings were making the T1 bonuses start at 0, and then increment from there so T2 would be the new T1 and T3 would be T2, etc, etc.

Is there potentially an issue with default/new install settings?

If you have had Circuit Processing mod enabled previously, it would have messed up your module settings. I'm almost finished updating Circuit Processing for 2.0 and this time I've done it in a way that won't affect mod settings.