Somehow it indeed finds an older version of the plugin on your system. I don't have it on Ubuntu, but below is what I get on Windows.
Notice that my V1.1.1 uses com.pemicro.debug.gdbjtag.pne_1.1.4.201409071615, can you check if you have that on your system?
Independently, I will ask around to check what could be wrong.
Thanks,
Erich
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P&E GDB Server, Version 5.07.00.00
Copyright 2014, P&E Microcomputer Systems Inc, All rights reserved
Loading library C:\Freescale\KDS_1.1.1\eclipse\plugins\com.pemicro.debug.gdbjtag.pne_1.1.4.201409071615\win32\gdi\unit_ngs_arm_internal.dll ... Done.
Command line arguments: -device=KE06Z128M4 -startserver -serverport=7224 -interface=OPENSDA -speed=5000 -port=USB1 -USE_CYCLONEPRO_RELAYS=0 -FORCE_MASS_ERASE=0
Device selected is ke06z128m4
User Specified Hardware Selection : Interface=OPENSDA and Port=USB1
Connecting to target.
OpenSDA detected - Flash Version 1.14
Device is KE06Z128M4.
Mode is In-Circuit Debug.
'Kinetis' is a registered trademark of Freescale.
(C)opyright 2012, P&E Microcomputer Systems, Inc. (www.pemicro.com)
API version is 101
Server running on 127.0.0.1:7224
Connection from "127.0.0.1" via 127.0.0.1
Copyright 2012 P&E Microcomputer Systems,Inc.
Command Line :C:\Freescale\KDS_1.1.1\eclipse\plugins\com.pemicro.debug.gdbjtag.pne_1.1.4.201409071615\win32\pegdbserver_console -device=KE06Z128M4 -startserver -serverport=7224 -interface=OPENSDA -speed=5000 -port=USB1 -USE_CYCLONEPRO_RELAYS=0 -FORCE_MAS
CMD>RE
Initializing.
Target has been RESET and is active.
CMD>CM C:\Freescale\KDS_1.1.1\eclipse\plugins\com.pemicro.debug.gdbjtag.pne_1.1.4.201409071615\win32\gdi\P&E\ke06z128m4_pflash_pipeline.arp
Initializing.
Initialized.
;version 1.02, 02/07/2014, Copyright P&E Microcomputer Systems, www.pemicro.com [ke_128k_pflash_ftmre_m0]
;device freescale, ke06z128m4, desc=pflash_pipeline
;begin_cs device=$00000000, length=$00020000, ram=$20000000
Loading programming algorithm ...
Done.
CMD>EM
Erasing.
Module has been erased.
Initializing.
Initialized.
;version 1.02, 02/07/2014, Copyright P&E Microcomputer Systems, www.pemicro.com [ke_128k_pflash_ftmre_m0]
;device freescale, ke06z128m4, desc=pflash_pipeline
;begin_cs device=$00000000, length=$00020000, ram=$20000000
Loading programming algorithm ...
Done.
CMD>PM
Programming.
Processing Object File Data ...
.
Programmed.
CMD>VC
Verifying object file CRC-16 to device ranges ...
block 00000000-000000BF ...
Ok.
block 00000400-00000CF3 ...
Ok.
Checksum Verification Successful. (Cumulative CRC-16=$3D37)
CMD>RE
Initializing.
Target has been RESET and is active.
Preset breakpoint encountered.