Transmitting APDUs in T=1 mode does not work because the native code always initializes a data structure for T=0. This leads to exceptions like the following:

javax.smartcardio.CardException: sun.security.smartcardio.PCSCException: Unknown error 0x16
    at sun.security.smartcardio.ChannelImpl.transmit(ChannelImpl.java:78)
    at ApduTest.main(ApduTest.java:51)
Caused by: sun.security.smartcardio.PCSCException: Unknown error 0x16
    at sun.security.smartcardio.PCSC.SCardTransmit(Native Method)
    at sun.security.smartcardio.ChannelImpl.transmit(ChannelImpl.java:73)
    ... 1 more

This is on Windows. I did not have a chance to test Solaris/Linux yet, but most likely it will not work either. This was not caught earlier because our test cards only support T=0.