I have now found a solution to this issue:-
Using Citrix Quick Launch and experimenting with some settings I was eventually able to generate an ica file that worked!
The key was using port 6669 on the citrix load balancer and changing the TcpBrowserAddress to HttpBrowserAddress.
6669 is the XML port. This is the one that is used to manage load balancing. So my ica file now looks like this and works!!!!
Note - this works for the 2008 Citrix servers farm using XENAPP 6.5
the same settings do not work for the 2003 Citrix Servers on XENAPP 4.5 which were working fine using the originl ica file using TcpBrowserAddrees.
[InputEncoding = ISO8859_1
[WFClient]
Version=2
EnableSSOnThruICAFile=On
ProxyType=Auto
HttpBrowserAddress=99.99.99.99:6669
ConnectionBar=0
[ApplicationServers]
65 Eclipse in QA=
[65 Eclipse in QA]
Address=65 Eclipse in QA
InitialProgram=#65 Eclipse in QA
ClientAudio=On
DesiredColor=4
DesiredHRes = 1024
DesiredVRes = 768
TWIMode = False
KeyboardTimer = 0
MouseTimer = 0
ConnectionBar=0
EnableSSOnThruICAFile=On
UseLocalUserAndPassword=On
TransportDriver=TCP/IP
WinStationDriver=ICA 3.0
BrowserProtocol=HTTPonTCP
Compress=On
EncryptionLevelSession=EncRC5-128
[EncRC5-128]
DriverNameWin32=PDC128N.DLL
DriverNameWin16=PDC128W.DLL
[Compress]
DriverName=PDCOMP.DLL
DriverNameWin16=PDCOMPW.DLL
DriverNameWin32=PDCOMPN.DLL
