Please don’t take my questions the wrong way, but since I am not on-site I have to ask.
Regarding the 25 pair Cat 3, are you really trying to run data over a 25 pair?
I would be willing to make a large wager none of this was ever tested. Since you can not test 25 pair cable for data. What exactly are you using 25 pair for? How is it terminated?
By using cat 3 instead of cat 5 you saved maybe .01 per foot and now you see why it may not have been a good idea.
As for the standards, cat 5 is no longer recognized, cat 3 is recognized for voice only. The standard is cat 6 at this time, although a lot of cat 5e is being installed.
All that being said....
Are your NIC's and router set for 10BaseT only? They should be since you are running cat 3, if they are auto-negotiating and trying to connect at 100BaseT I would suspect this to be the problem.
Are you switches truly switches or hubs? Since you have switches in remote locations, how are they connected to the Router?
Cat 3 is VERY susceptible to EMI, do you have adequate separation between your cable and fluorescent lights and motors?
In the future I would use nothing less than cat 5e 4 pair cables for anything that data will transmit on, you don’t save ANY money by cutting corners on cable…cable is the cheapest part of the installation.
Richard S. Anderson, RCDD