When you buy back one of your saved ship presets it seems that addons are attached to the lowest numbered port (of the correct type) rather that the port used from the original preset.

How to reproduce bug: Buy a Ragnorok and assign a small weapon to port 3 (port-side small port) and large weapon to port 6 (rear large port) and add a battery. Assign the weapon groups such that primary trigger fires port 3 and secondary trigger fires port 6. Now save the preset.

When you buy back the preset the small weapon will now be in port 2 (front small) and the large weapon will be in port 5 (front large), but the triggers are still assigned to ports 3 and 6 so if you launch the triggers won't do anything.

I looked at how the preset was saved to the config file, and it exactly matched my loadout, including correct port assignments. Here is an example preset:
shippreset1=ports={188024242,0,2150363876,0,0,2412111308,0},groups={{[3]=true},{},{},{},{},{},{[6]=true},{},{},{},{},{},{},{},{},{},{},{}},shipcolor=105,ship=3026614685

After trying to buy back the original preset, I resaved what was purchased to preset 2. Here is what was saved (notice the port assignments are different):
shippreset2=ports={188024242,2150363876,0,0,2412111308,0,0},groups={{[3]=true},{},{},{},{},{},{[6]=true},{},{},{},{},{},{},{},{},{},{},{}},shipcolor=105,ship=3026614685

Hm, interesting. I'll see if I can fix this for Friday. Thanks.

This is fixed in the next client update.