I've attached a character that demonstrates the issue for me. For the attached character, the attacks should be:
Rapier: +1 BAB + +5 DEX = +6
Light Hammer: +1 BAB + +5 DEX = +6
Light Hammer (Ranged): +1 BAB + +5 DEX = +6
Your list doesn't include any improvised weapons. Unless you believe that any non-proficient weapon is considered "improvised", which is not how I understand the rules - Improvised Weapons: Sometimes objects not crafted to be weapons nonetheless see use in combat. Because such objects are not designed for this use, any creature that uses an improvised weapon in combat is considered to be nonproficient with it and takes a –4 penalty on attack rolls made with that object. To determine the size category and appropriate damage for an improvised weapon, compare its relative size and damage potential to the weapon list to find a reasonable match. An improvised weapon scores a threat on a natural roll of 20 and deals double damage on a critical hit. An improvised thrown weapon has a range increment of 10 feet.
Benefit: You do not suffer any penalties for using an* improvised melee weapon*. Unarmed opponents are flat-footed against any attacks you make with an improvised melee weapon.
Normal: You take a –4 penalty on attack rolls made with an improvised weapon.
I see no bug here.
You're quite right about nonproficiency versus improvised weapons, and I think that goes a long way towards pointing to where the bug actually lies.
The issue, rather, is that the Monk of the Empty Hand's class feature- whereby all weapons are treated as improvised weapons- does not seem to be applied: "A monk of the empty hand treats normal weapons as improvised weapons with the following equivalencies (substituting all of their statistics for the listed weapon): a light weapon functions as a light hammer, a one-handed weapon functions as a club, and a two-handed weapon functions as a quarterstaff. This replaces the normal monk weapon proficiencies." (from http://paizo.com/pathfinderRPG/prd/advancedPlayersGuide/coreClasses/monk.html)
Incidentally, James Jacobs wrote that Monk of the Empty Hand should also not receive a penalty on the use of improvised weapons, like with catch off-guard: http://paizo.com/threads/rzs2l7ns&page=114?Ask-James-Jacobs-ALL-your-Questions-Here#5683 (This isn't relevant in my test case, since I do have the feat; but as long as we're looking at this, it's important to bring up. However, I'm not sure on the pcgen policy/standard for applying 'clarifications' like this; perhaps implement it as a house rule?)
You certainly went a very round about method to say that an Archetype is not working with a feat.
Utilizing weapons (regular weapons) and declaring them improvised is not a logical function in PCGen. As strange as this will sound, you're asking for a Feature Improvement, not a bug fix. To my knowledge, there is no "improvised" weapons that exist in pcgen. Most people do not usually hamper themselves with penalties. Using a chair leg in combat for a single encounter is usually handled at the table, not something people ask for.
You are asking that I include a new group of weapons "Improvised", and in your archetype's corner case, include three specific new improvised weapons to cover it's variant on the rules. On top of that, you want these improvised weapons to get the benefits of said feat earlier referenced. You also want me to arbitrarily alter the damage and other stats of "regular" weapons in your archetype's hands - sorry, not gonna happen. I am not going to spend 12+ hours crafting elaborate data hacks just so you can select any weapon and have the values reflect one of three weapon categories.
Ergo, not going to be a high priority compared to say Occult Adventures, Path of Shadows and the 7 pending book reviews I have to get handled.
Bug = A feature that is implemented in pcgen but not functioning as intended. Since Improvised Weapons do not exist, I can hardly believe there is any code involved. Hence nothing coded or implemented.
When I get around to this, you'll have the regular improvised chart, and then your archetype will have access to the three listed items.
I apologize; I definitely wasn't trying to be difficult; but it wasn't initially clear to me what bonus I was losing. The troubleshooting render unfortunately doesn't show nonproficiency penalties; I was so focused on the character I was building that I didn't consider that the class feature may not have been implemented. Would it be reasonable to ask that a note be added to the class feature to indicate as much?
As far as implementing the class feature, I understand the complexity involved and I don't mind the (very) low prioritization. This is obviously an infrequent case, so I do think it would definitely make more sense to wait (albeit possibly forever) for code support that allows this to be implemented more cleanly.
The addition of improvised weapons as a type of equipment sounds excellent, as does the addition of the three types called out by the class feature; though perhaps it would be simpler to just grant the class proficiency in Light Hammer, Club, and Quarterstaff.
In either case, it seems like implementing improvised weapons as an exotic weapon (at least in the sense of- not basic or martial, thus not automatically on any class's proficiency list; I don't know if pcgen has an internal weapon type that could represent this) could ease implementation of the Catch Off-Guard feat itself, since it now just needs to add a note on attacks; and grant proficiency in improvised weapons.