"recently we have been having major problems"

What did you change?

"variables being overwritten for no apparent reason"

Does your toolset use data overlaying?
You would see this sort of symptom if you had messed-up overlaying!

"There is no reason I can think of..."

Doesn't necessarily mean that there is no reason! ;-)

"I suspect the mess above was a workaround that the person who did the original work did to get around some sort of problem..."

Of course, having suffered the frustration, you will be sure to carefully write it all up and document what you did and why you did it... ;-)