So, someone else has changed a variable in your situation, and you are getting a different result than what you have previously experienced. When I see someone make a statement like this (do not take this personally!), it usually means that they lack the prerequisite field skills set and hardware to figure out what has changed, and it is not something that someone on the internets can tell you how to make a quick fix.
As this is for a fire dept and you just took over "some radio maintenance", you should call a qualified and trained radio shop to resolve your issue. If you decide to hack away at it on your own, when your station misses a call entirely, gets retoned, etc and there is a significantly negative outcome after your delayed or missed-entirely response...they are coming after you. You want that? Can you afford to represent your agency on your own?
You should call whomever services your radios and inform them of that problem. There are TENS to HUNDREDS of variables that you will be forced to post on here (most of which will initially be confusing to you - as you may not fully understand what people are asking of you to provide) before those of us that can diagnose / fix that problem for you can help.
This is not "some radio maintenance", this is "system infrastructure modification". Seek professional help from a qualified professional provider who carries appropriate insurance and has the training to do it right, and will continue to work at it until problem is resolved.
All that being said...I had the exact same thing happening to an agency I used to work for. After a tone activation, the station alerting system stayed unmuted for a length of time, and a distant (yet co-licensed) frequency user went digital, and we heard their digital transmissions. I can virtually guarentee that is what is happening to you.