I'll preface this by saying I know very little about Swashies...
There are a few areas that are different between bots and players with how they approach fights.
First, as a player you can pop your 'temp' buffs on incoming and move behind the mob. Bots don't. They don't have any real concept of 'incoming'. They sit and wait (probably till the mob is 99% or 98% health) and then start doing their thing. On non-named fights, this can account for a pretty significant portion of a fights time and can hurt your DPS quite a bit.
Second, as a player, you have an idea of how long a fight will last. Bots don't. This means a bot will use a big long dot when a mob is at 1% health, cast a long temp buff just before the fight ends, or put a debuf on the mob just before it dies. Something a player would only due by mistake. This can also hurt your apparent DPS on act. About all the bot has is the Heroic CAs and regular CAs tabs.
Bots rebuff everything on death. If someone dies, bots will stop and rebuff themselves and the rest of the group. You need to be careful about the two boxes for in combat and out of combat buffs. The group buff tab, soon as you are rezed you're bots going to go through that list, regardless of what else is going on. As an example, soon as your swashy is rezzed, he is probably going to reapply his hate transfer back on the tank, even if the mob only has 10% health left. This is more lost DPS and something you might wait to do till after the fight.
As well, Bots don't really know what the other bots are doing. Thus, they don't know that TimeWarp is coming in 10 seconds, or that dispatch just fired, etc. This can also be lost DPS for your toon.
Most of the above only really matter for short fights. Longer named fights, the time lost due to the above items is pretty minimal in the overall length of the fight.
The biggest area, and what is probably hurting your Swashy's DPS the most, is the CA, heroic CA, and Chain tabs. I haven't seen a lot of other people post here who appear to play a swashy, so my guess is those tabs could use a bit of work. They are probably decent but not as good as the order you are choosing for yourself.
Look at the CA tab. The bot will always 'click' the highest available ability in this list it can. So for the 10th item on the list to be clicked, items 1-9 all have to be unavailable (grey'd out). Go through the CA tab and try to get the casting order to replicate what you do yourself. I generally set mine up in the following way for DPS toons...
AE debuffs ( only cast in AE fights )
AE attacks ( only cast in AE fights )
Single target debuffs ( always used )
Single target attacks ( always used )
Check your long running dots and debuffs against the maintained flag. This will keep the toon from 'clicking' the ability again if it is already running. Most debuffs you want maintained. Dots you probably want to reapply.
One of the best ways to do this is to go find a training dummy. Fight it yourself, see what you cast and what order. Then have the bot do it and see what it casts in what order, and fix what you don't like. The Debug messages to the bot console are very helpful with this, but just watching the bots casting bar can help alot.
Lastly, a few other points...
Make sure your bot isn't trying to buff something and failing. They don't know about 'concentration slots' or how many of buff X they can do. They will just try to cast it over and over again. This will really hurt your DPS. The debug settings are your friend for finding this out.
Make sure your bot has auto attack timing turned on.
Make sure your bot is running behind the mob and has his stealth attacks setup right.
Can't really hurt to run an 'ogre spellexport' just to make sure everything is in sync.
Check the bots CA order and see if some of those aren't firing for some reason as you'd expect. Perhaps there is a stealth or rear attack in there which isn't setup right so the bot keeps skipping it.
Classic Coke