You must disable both hardware and software flow control when communicating to the bootldr.
The iPAQ H3600, iPAQ H3100 and iPAQ H3700 do not support hardware flow control as a data communication device, although it does support hardware flow control as a data terminal. In other words, when you connect the iPAQ to a modem, you may use hardware flow control, but not when you connect it to another computer.
This hardware limitation has been fixed in the iPAQ H3800See the H3800 Linux Port Status Page for details on this port., although it is still unsupported by the bootldr.
If you are using minicom on the host PC, make sure that the lrzsz package is installed.