You did nothing wrong Mordor. As long as you are 1.3.2 on the RC and 1.4.0 on the aircraft, it's all good.
Have you upgraded the batteries?
I only have one battery, so i presume the 1.4fw did also update the battery automatically..
I have backup of the logs:
[00012597]========== 2014.01.01 00:00:12 unsynchronized ======
[00012613]Packet [C:\P3S_FW_V01.04.0010.bin] detected.
[00012617]Packet upgrade start...
[00012625]Packet checking...
[00012630]Done.
[00012636]Version checking[1]...
[00012670][03 05] v34.2.0.8 -> v34.2.0.9 need upgrade.
[00012710][03 06] v2.1.6.18 -> v2.3.0.13 need upgrade.
[00012720][04 00] v1.36.0.0 -> v1.41.0.0 need upgrade.
[00012738][09 00] v1.7.0.3 -> v1.7.0.3
[00012809][11 00] v1.6.1.0 -> v1.7.0.0 need upgrade.
[00012859][12 00] v1.8.0.0 -> v1.10.0.0 need upgrade.
[00012903][12 01] v1.8.0.0 -> v1.10.0.0 need upgrade.
[00012943][12 02] v1.8.0.0 -> v1.10.0.0 need upgrade.
[00012978][12 03] v1.8.0.0 -> v1.10.0.0 need upgrade.
[00012987][15 00] v1.1.2.0 -> v1.1.2.0
[00013033][17 00] v1.1.1.2 -> v1.1.1.7 need upgrade.
[00013113][17 01] v1.0.2.4 -> v1.0.2.7 need upgrade.
[00013138][19 00] v1.0.8.96 -> v1.0.8.96
[00013144][01 00] v1.7.2735 -> v1.21.3647 need upgrade
[00013149][01 01] v1.7.2735 -> v1.21.3647 need upgrade
[00013155]Done.
[00015159]Waiting for user confirm...
[00025165]Timeout, start upgrade automatically.
[00025175]Firmware upgrading[1]...
[00038647][01 00] Firmware upgrading start...
[00011737][01 00] Firmware upgrade finished successfully.
[00011845]Done.
[00011876]Packet [C:\P3S_FW_V01.04.0010.bin] resumed, card sn [0x90ce6ced].
[00011911]Packet vlink 01.04.0010 <-> 01.03.0020.
[00011974]Version checking[2]...
[00012023][03 05][00] v34.2.0.8 -> v34.2.0.9 need upgrade.
[00012084][03 06][00] v2.1.6.18 -> v2.3.0.13 need upgrade.
[00012120][04 00][00] v1.36.0.0 -> v1.41.0.0 need upgrade.
[00012173][09 00][00] v1.7.0.3 -> v1.7.0.3
[00012264][11 00][00] v1.6.1.0 -> v1.7.0.0 need upgrade.
[00012327][12 00][00] v1.8.0.0 -> v1.10.0.0 need upgrade.
[00012417][12 01][00] v1.8.0.0 -> v1.10.0.0 need upgrade.
[00012497][12 02][00] v1.8.0.0 -> v1.10.0.0 need upgrade.
[00012572][12 03][00] v1.8.0.0 -> v1.10.0.0 need upgrade.
[00012607][15 00][00] v1.1.2.0 -> v1.1.2.0
[00012667][17 00][00] v1.1.1.2 -> v1.1.1.7 need upgrade.
[00012768][17 01][00] v1.0.2.4 -> v1.0.2.7 need upgrade.
[00012812][19 00][00] v1.0.8.96 -> v1.0.8.96
[00012845][01 00][05] v1.21.3647 -> v1.21.3647
[00012876][01 01][00] v1.7.2735 -> v1.21.3647 need upgrade
[00012907]Done.
[00012936]Firmware upgrading[2]...
[00013074][01 01] Firmware upgrade start...
[00043329][01 01] Firmware upgrade finished successfully.
[00043374][12 00] Firmware upgrade start...
[00109232][12 00] Firmware upgrade finished successfully.
[00109280][12 01] Firmware upgrade start...
[00171917][12 01] Firmware upgrade finished successfully.
[00171964][12 02] Firmware upgrade start...
[00239672][12 02] Firmware upgrade finished successfully.
[00239720][12 03] Firmware upgrade start...
[00303885][12 03] Firmware upgrade finished successfully.
[00303940][17 00] Firmware upgrade start...
[00419387][17 00] Firmware upgrade finished successfully.
[00419430][17 01] Firmware upgrade start...
[00485411][17 01] Firmware upgrade finished successfully.
[00485450][11 00] Firmware upgrade start...
[00534506][11 00] Firmware upgrade finished successfully.
[00534553][03 05] Firmware upgrade start...
[00602346][03 05] Firmware upgrade finished successfully.
[00602651][03 06] Firmware upgrade start...
[00940530][03 06] Firmware upgrade finished successfully.
[00940591][04 00] Firmware upgrade start...
[00997085][04 00] Firmware upgrade finished successfully.
[00997119]Done.
[00997151]Version checking[3]...
[00997221][03 05][05] v34.2.0.9 -> v34.2.0.9
[00997301][03 06][05] v2.3.0.13 -> v2.3.0.13
[00997350][04 00][05] v1.41.0.0 -> v1.41.0.0
[00997395][09 00][00] v1.7.0.3 -> v1.7.0.3
[00997501][11 00][05] v1.7.0.0 -> v1.7.0.0
[00997595][12 00][05] v1.10.0.0 -> v1.10.0.0
[00997694][12 01][05] v1.10.0.0 -> v1.10.0.0
[00997774][12 02][05] v1.10.0.0 -> v1.10.0.0
[00997849][12 03][05] v1.10.0.0 -> v1.10.0.0
[00997882][15 00][00] v1.1.2.0 -> v1.1.2.0
[00997969][17 00][05] v1.1.1.7 -> v1.1.1.7
[00998089][17 01][05] v1.0.2.7 -> v1.0.2.7
[00998135][19 00][00] v1.0.8.96 -> v1.0.8.96
[00998166][01 00][05] v1.21.3647 -> v1.21.3647
[00998199][01 01][05] v1.21.3647 -> v1.21.3647
[00998230]Packet upgrade finish successfully.
Did i update the battery?