I can't say for sure with your particular model universal recharger / battery but:
I have used other uni-rechargers (talking 'bout a device that attaches directly to a battery and its terminals, not charging though a cell or laptop's internal mechanism). In the cases I tried them I found that they did 'work', but never worked as well as the OEM mechanism. They would only partially charge, hard to get to charge, or had other oddities. Without seeing your equipment in hand, I'd say what your describing is about similar to what I got with them.
These batteries and their chargers have their own special circuitry designed for optimum performance. Especially in the case of laptops, the batteries themselves have their own circuitry to assist charging, load, and report health. The laptop's power circuitry is designed to work with these batteries' functions. It's not so easy to just bypass it all and expect stock reliability.
Some OEM make external chargers, I'd go for that. I did a quick search and could not find one for Toshiba. Perhaps a Dock would work. If the dock has its own power port, it might be enough to power and charge the laptop and battery while docked. That I can think of.. that or get a new mainboard or laptop. I don't know your model laptop, but this dock does have its own power port, for a mere $189:
http://www.toshibadirect.com/td/b2c/adet.to?poid=422067Hope that helps,
Strat