i put your files into one file and didn't have any trouble compiling it with the chisel C++ backend. i'm really not sure why you are having trouble.
run patmos-test
run patmos-test
[info] Compiling 1 Scala source to /Users/jrb/Documents/bar/flo/sbt/flo/target/scala-2.10.0/classes...
[info] Running Flo.Main patmos-test
PATMOS TEST
// COMPILING Patmos(1)
started inference
7
finished inference
start width checking
finished width checking
started flattenning
52
finished flattening
resolving nodes to the components
finished resolving
BEGINNING COMBINATIONAL LOOP CHECKING
BEGINNING SEARCHING CIRCUIT FOR COMBINATIONAL LOOP
FINISHED ANALYZING CIRCUIT
NO COMBINATIONAL LOOP FOUND
total: 54
name: count %
Extract: 9 40.91
Mux: 3 13.64
Reg: 3 13.64
+: 2 9.09
|: 2 9.09
~: 1 4.55
##: 1 4.55
&: 1 4.55
w: count %
8: 9 40.91
10: 4 18.18
1: 4 18.18
33: 3 13.64
7: 1 4.55
32: 1 4.55
f: count %
1: 20 90.91
3: 1 4.55
5: 1 4.55
NUM 22 MAX-WIDTH 5 MAX-DEPTH 8
g++ -c -o ../emulator/Patmos-emulator.o -O2 -I../ -I/Users/jrb/Documents/bar/chisel/csrc/ ../emulator/Patmos-emulator.cpp RET 0
g++ -c -o ../emulator/Patmos.o -O2 -I../ -I/Users/jrb/Documents/bar/chisel/csrc/ ../emulator/Patmos.cpp RET 0
g++ -o ../emulator/Patmos ../emulator/Patmos.o ../emulator/Patmos-emulator.o RET 0
STARTING ../emulator/Patmos
---
INPUTS
INPUT(instr_a) = 0
INPUT(Patmos__pc.Patmos) = 0
OUTPUTS
READ OUTPUT(Patmos__io_led.Patmos) = 254[0xfe] ( Flo.Patmos$$anon$1.<init>(patmos.scala:82) )
READ OUTPUT(Patmos_fetch__io_out_instr_a.Fetch) = 131327[0x000200ff] ( Flo.FetchOut.<init>(patmos.scala:18) )
READ OUTPUT(Patmos_fetch__io_out_pc.Fetch) = 0[0x000] ( Flo.FetchOut.<init>(patmos.scala:21) )
READ OUTPUT(Patmos__pc.Patmos) = 10[0x00a] ( Flo.DecodeOut.<init>(patmos.scala:31) )
led/litVal 254
pc: 0
pc decode: 10
---
INPUTS
INPUT(instr_a) = 0
INPUT(Patmos__pc.Patmos) = 0
OUTPUTS
READ OUTPUT(Patmos__io_led.Patmos) = 253[0xfd] ( Flo.Patmos$$anon$1.<init>(patmos.scala:82) )
READ OUTPUT(Patmos_fetch__io_out_instr_a.Fetch) = 262145[0x00040001] ( Flo.FetchOut.<init>(patmos.scala:18) )
READ OUTPUT(Patmos_fetch__io_out_pc.Fetch) = 1[0x001] ( Flo.FetchOut.<init>(patmos.scala:21) )
READ OUTPUT(Patmos__pc.Patmos) = 10[0x00a] ( Flo.DecodeOut.<init>(patmos.scala:31) )
led/litVal 253
pc: 1
pc decode: 10
---
INPUTS
INPUT(instr_a) = 0
INPUT(Patmos__pc.Patmos) = 0
OUTPUTS
READ OUTPUT(Patmos__io_led.Patmos) = 251[0xfb] ( Flo.Patmos$$anon$1.<init>(patmos.scala:82) )
READ OUTPUT(Patmos_fetch__io_out_instr_a.Fetch) = 393218[0x00060002] ( Flo.FetchOut.<init>(patmos.scala:18) )
READ OUTPUT(Patmos_fetch__io_out_pc.Fetch) = 2[0x002] ( Flo.FetchOut.<init>(patmos.scala:21) )
READ OUTPUT(Patmos__pc.Patmos) = 10[0x00a] ( Flo.DecodeOut.<init>(patmos.scala:31) )
led/litVal 251
pc: 2
pc decode: 10
---
INPUTS
INPUT(instr_a) = 0
INPUT(Patmos__pc.Patmos) = 0
OUTPUTS
READ OUTPUT(Patmos__io_led.Patmos) = 247[0xf7] ( Flo.Patmos$$anon$1.<init>(patmos.scala:82) )
READ OUTPUT(Patmos_fetch__io_out_instr_a.Fetch) = 34087296[0x02082180] ( Flo.FetchOut.<init>(patmos.scala:18) )
READ OUTPUT(Patmos_fetch__io_out_pc.Fetch) = 3[0x003] ( Flo.FetchOut.<init>(patmos.scala:21) )
READ OUTPUT(Patmos__pc.Patmos) = 10[0x00a] ( Flo.DecodeOut.<init>(patmos.scala:31) )
led/litVal 247
pc: 3
pc decode: 10
PASSED
[success] Total time: 2 s, completed Feb 20, 2013 11:23:25 AM