I'm finding that alot of my weapon hits aren't causing damage to a ship. I can generally get a ship to 50% damage but I pound it at close range and it takes many hits to destroy it. The shield effect doesn't happen and you get the explosion sound effect but there's no damage caused.
I know there was a problem similar to this when running the non-gog version on a fast machine, but I never experienced it myself and was wondering if this is the same thing.

Maybe you're shooting too fast? Sometimes the screen says "PCB Overheat" and while it will shoot, it will do minimal damage. Give it a few seconds.

Oh man, I'd hoped that this problem wouldn't show up in the Gog version. I encountered it a couple of years back when trying to get my original version to work. This is the anwers I got on the Atari forums and I'm pretty confident of it given whom it came from.
http://www.ataricommunity.com/forums/showthread.php?t=628573
By the way, I never got the game to properly work using that advice. But that might just be because I'm not terribly good with computers.

I'd be interested if anyone else has the same problem with the GOG version. I never encountered the problem myself, but I do remember others having it.
The trouble is that if the problem is there I don't know how they can fix it. The game was never designed to run over 100fps internally, but on modern machines it can do just that, which is what caused the original weapon hit problem in the first place.
It's ironic really if If it's just the PBCs overheating because I worked on the game, and you'd think I'd know how to play it! But I've not been able to play it for years due to the incompatibility problems, so I'm grateful to GOG for getting the game working as well as they have.

Running the game using the dgVoodoo glide wrapper at high res seems to have improved things. I'll need to test a bit more to make sure.

I'm not really sure that my post warranted being marked as a "solution", but it's great if it's working properly for you now!
IF it really is just a case of dgVoodoo causing the computer enough extra work to avoid the issue, then that sounds like an awfully temporary sort of solution, and I would have to guess that the issue would simply be raised again when running on an even faster machine.
OTOH, if that internal counter is somehow tied to the visual frame rate, and the latter is being reliably limited by dgVoodoo, then maybe it really does solve the problem?
I was having another look at the Atari forums, and noted this post about using the Windows Application Compatability Toolkit to slow down the CPU. I was wondering whether this might be a handy way to prevent I-War from running too fast?
http://www.ataricommunity.com/forums/showpost.php?p=6151440&postcount=14

For some reason the forum went a bit bonkers on me and accidentally marked your post as a solution unfortunately. Is there any way to change it?
After playing a few more missions it seems much improved using the new wrapper. Certainly most hits on an unshielded ship seem to cause damage now, and the game seems easier.
Plus of course the advantage is that you can run the game at high res and it looks much, much better.

Are there any Glide wrappers with adjustable frame limiters? dgVoodoo doesn't really improve things much for me, even with VSync on.
On the plus side, it looks brilliant in 1600x1200.

I think my main problem was firing during PBC overheat. Waiting for the PBCs to cool down a bit seems to fix most of the problems.
However some big ships take a lot of hits to damage them, and they do repair fairly quickly. The best way to deal with this is to subtarget the ships and blow up their individual systems one by one. Missiles are especially useful for doing that. This makes it much easier to destroy a large ship.

Oh, just now found this thread. I think I might be having this problem:
http://www.gog.com/en/forum/independence_war_series/double_front_pbc_not_doing_damage

Has anyone else encountered this with the GOG version? Any suggestions?

I know this is incredibly late, but I figured I'd shed some of my own light on this, especially as an apology to Ravenger for being a jerk about Impeachment 2.

This issue wasn't as bad as it is now in the non-GOG version, but here, you can at least partially remedy this by alternating fore and aft PBC cannon. It may or may not be an FPS issue, since the alternation works... but then again this is just the hypothesis of someone who has no idea about how the game or the glide wrapper works. :V

I can confirm that that was the problem for me.
To solve it i limited the framerate with nglide 1.05

edit: This didn't solve the problem it just reduced it.

The bundled nglide wrapper (makes the old 3dfx games run on modern drivers) didn't apply the framecap so i updated this first from:
nglide wrapper

- download and run nglide_1.05_setup.exe
- uninstall nglide 1.02 by deleting (or moving) the files glide2x.dll and glide3x.dll from your i-war insallation folder
- start the configurator: win key-> type "nglide configurator" make sure the window state version 1.05
- set Vertical synchronization to ON and Refresh rate to 60 Hz
- Apply

don't forget to give feedback if it worked (more importantly if it didn't)

I remember the last time I played I-War back in like 2008 or something I had a lot of grief with this problem, which made WEP Advanced II impossible to complete for me because of that carrier.

I managed to defeat the problem mostly by setting an external 30fps cap from my graphics card settings - then again, I still occasionally get "glancing blows" that do nothing (especially on S-Fighters for some reason), but normally getting a bit closer and shooting them again does the damage.

Using the antimatter injector makes my hits far more likely to actually do damage too... Hmm.

Thanks for that follow-up. I've not tried it, but to me this sounds like an upgrade that GOG should consider making to their version of the game. If you've not already done so, could you raise a support request about it? Does the GOG version not still use Zeckensack's Glide wrapper? It certainly did originally, and there's no changelog for the game indicating a switch to nGlide.