RTL8139 are in fact PCI chips, did you mean you get one on ISA? Vendor, model number, please?
Any supported PCI cards (including RTL8139-based) are detected automaticaly, on RouterOS since long time ago (but I did not check in 2.9beta1 - try stable version first), so if it is a PCI card, the problem is in hardware (swap PCI ports, try different cards). Consult the Device Driver List for the actual list of supported chipsets:
http://www.mikrotik.com/docs/ros/2.8/gu ... t.frameset