I think it may be the reason of interface. However pay some attention to the pynq framework may aslo work because sometimes the reason for error could be very simple.
I make a artificial neural network(ANN) model by HLS IDE and integrated it in in Vivado and then transfr the .bit in pynq. The model perform bad in pynq board.
even it perform well in HLS IDE simulation:
I define interface in axi interface for teatures vector input, and then get the interface result with axilite interface. Please ignore the out interface, I use them for debug.