I would not immediately suspect that the receiver to be faulty, especially if it seemed to work ok when you were using split transmit and receive antennas. That said, using a service monitor, you'd need to first measure the receiver’s sensitivity with it isolated from the duplexer to determine if its sensitivity meets specifications.
On the surface, it sounds more like you have receiver desensitization since migrating from split antennas to use of the duplexer. What is the
make and model of your duplexer and what is your frequency split? Keep in mind that the VHF Quantar's receiver preselector is approximately 4 MHz wide and is specked for a separation of approximately 1.5 MHz when using a typical duplexer.
If you're using the Quantar for a two-meter harm repeater with only 600 KHz of separation, then you're going to need a lot more duplexer isolation that what you were accustomed to when using with older repeater stations that had narrower front-end designs. Of course, you may
have transmitter noise or something in your transmission system that is contributing to desensitization aside from duplexer isolation.
Again, the only way to determine the problem with the apparent lack of sensitivity is to trouble shoot the system using a service monior to test the receiver stand alone and in full duplex operation with and without the antenna and transmission line connected.
BTW, an SWR of 1.49 is not all that good in that you only have about 14 dB of retrun loss and whereby the mismatch in load impedance may
contribute to a reduction in duplexer insertion loss and isolation performance.