helo qpit3a,
I think, your design has a gndproblem and a power supply problem.
Comperators like the LTC1720 will drar a high current peak during switching, therefore it is needed to have a batery of caps close to the supply pins. I modified your design here and addes 2 caps 10n and 1µ.
general the caps for for bypassing the chips are to fare away from the power supply pins in your design. do also not switch the layer when connecting bypass caps this adds aditional inductivity to the trace that reduces the bypassing ippact of the cap. connect always 1st the pad of the bypass cap from the power rails and than connect the power pin direct from the pad of the bypass cap. do not connet the power inbetween the the two pads.
I also changed to all SMD design exept of the BNC jacks.
I used 1N4148 as input protection (did not have the correct footprit for that)
Separate signal and power GND. With high current peaks on power rails you impact the signal GND and so your signal as well.
place a GND plane for signal GND on top and bottom Layer. place a lot of stiching vials on the GND planes
if possible go to 4-Layer design. here place GND layer as 2nd Layer for PWR GND and 5V Plane as 3rd Layer.
I also redra your schematic, as yours is not very good to read. I mostely build the library smbols myself, as the parts suplied in the lib are usually ugly. I also separate power connection and and functional gates: here the double comparator with 2 seperate comperator symbols and a seperate power symbol. I also put aditional notes on the schematic, her I calculated the gain of the preamplifier and the hysteresis of the comparator. this helps during initial operation of the circuitry.
So at the end I hafe a question to you: for what ist this preamp used for? Will it be used as input section for µC counter input?
It helps also, to decouple the power from the comparator with an aditional inductivity.
Here infos on bypassing, have also a look on part 2 and 3 (link at the end) and
here Analog Devices App Note MT-101 you find aditional hints.
Guido