Ok Wing I had that problem too. What you have to do is a bit tedious but it works. Always check your fleet status after leaving base, if you get a blanked out space on any of your ships then quit game & reload from your autosave (which will be the latest save) and usually all the ships are listed & will remain listed. However you kinda have to make sure you get to base on a regular basis to keep your autosave up to date.
Other problems to save you from 1 don't go to base in any of your captured fleet ships or you loose it for some reason. 2 If you want your fleet in a hurry to a major fight, wait for them to catch up (which can be awhile)a few km from where fight is. 3 Always remember to jump back to your main ship after a capture or else when you go back to base #1 happens. 4 This of course also tells you you can't customize any of your captured ships at base, so chcek your ships before you capture them. No sense catching a corvette with 1 lousy quad light gun. 5 If you don't have a lot of memory combining mods can be a problem and you get crashes. 6 Yep no ifleet in act 1. 7 Yep you could have a zillion ships, seems you can only use 1 to dock and try to get a ship. So remember fighters 1 defender, intercepters 2, tugs 5, patches 10, corvettes 15, cruisers 85 Seems you can't get transports or utilities which in theory could carry a bunch of marines to capture a ship. But hey all in all for an experimental mod, ifleet is pretty good:)
Most of this stuff I found out the hard way:)
Ok that's passing on experience so others don't get into this bind or exercises in frustration.
The Ram Ship 
