valve off make up and bypass and see if you still have problem. B&G says to close outlet of prv when system is filled. could it also be just a leaking relief? not much else going to cause this problem besides what has already been stated.
Two weeks later and this problem still exists? I'm surprised you, or your boss, haven't already called in someone who is experienced with this type of system. The systems like this that I have seen either are in the cooling mode (water flow directed to cooling tower for heat rejection), or in the heating mode (water flow directed to the boilers for a heat source). Not both at the same time. The fact that you are seeing the same pressure (45 psig) at the cooling tower and the boilers at the same time indicate that either flow is directed to both, or neither. The fact that both those pressures are equal to pump discharge pressure indicate that there is no flow at all. Pressure should decrease, overall, as distance from pump increases. With allowances for variations due to height. You should be using one gauge, moved from tap to tap, to eliminate gauge error. If you have verifiable good gauges, then you can probably rely on multiple gauges to check for presence of pressure changes. But I would not rely on seperate gauges to tell me how much that change, or difference, is. Strictly one guage for that. For what it's worth, I suspect that while draining and refilling the system, a valve or two was overlooked and is in the wrong position. Maybe it's linkage (including internal) broke and it is not in the position you think it is. A shut valve, or any type of flow restriction, will have a significant pressure drop across it.
Is there a heat exchanger anywhere? Usually this type of system has two water loops/ 1 loop is simply the boiler heated water to a heat exchanger with a separate pump. This exchanges heat to the building water supply loop which uses its own pump(s) to supply building wshp 's . In summer a diverting or bypassing valve setup is used to bring water to towers only. Usually a boiler is a lot lower operating pressure than the building loop but if the two systems are being allowed to mix somehow, then you've got a problem. Don't forget the tower feeds are connected to potable street pressure water and you can't have that entering a boiler. Check your boiler feed and expansion tank also then check all system valves for proper operati g position. If your heat exchanger has even the most minute leak allowing transfer of pressure from one loop to the other you'll have a problem
I think you have a heat exchanger somewhere that your missing. As some one else has already stated, these types of system usaully have a closed loop for WSHP and that closed loop is either directed to exchanger or to cooling tower depending on loop temp. You may have just overfilled your boiler when filling, did you use the bypass to fill?
Several people have asked about height of the loop. You haven't given that. The reason we are asking is because the water pressure in the system adds up. If you have a system 40 ft vertical you will see .433 psi/ft so 17.3 psi static just to get to the top of your system plus your 12 psi is about 30 psi system pressure. Is the boiler and expansion tank in a penthouse (top of the loop) or on a lowest point. Ultimately you said the pressure increases when boiler fires which leads to expansion tank. These tanks need to be pressurized to system pressure with the tank out of the system. The 12 psi it may have been set to when it was new may not be what is needed. You said the tank was okay because you drained it. Do you have an expansion tank or compression tank?