There are also numerous ways around this issue. Specifically the /Virtual flag. One reason that it was difficult is because of the thousands of extra features that Toad has that many other programs do not. Specifically, the automatic saving of your settings x number of minutes. Most programs do not have this but Toad does (requested by users) and this can cause issues if you have multiple instances open because you're saving to the same location. We've also solved this issue with the /virtual command line parameter but it was introduced in 12.7. Since you're running a version that is several years old, it's very possible you don't know about the changes and enhancements that have occurred.
Also, are you running queries in threads (an option)?
Are you running things as a scrip (F5)t? If so, we have to wait for the script to complete before returning control. If you have a long running script, execute via QSR or SQL*Plus to get control back.
Have you looked at connection colors to keep track of what is dev and what is prod?
Also remember that Toad was designed a very long time ago when MDI was the way. We have looked at alternatives but given the user base and the effort required, it's not really a viable option. Look at the nightmare M$ created for themselves when they redesigned Office to have ribbons. They can get over it because they have infinite resources and a monopoly on the space. Most companies simply can not toss their app into the garbage heap and start over. We're constantly trying to improve and will continue to improve things but posting an insult ridden tirade on a three year old post is not helpful at all.