Hi Dan,
great to hear that your idea works!!! 
Hi Chriss,
I wrote that you found the solution and thought that it was clear that the pinning has to be changed for STEC16B… however, in the meantime I tried the encoders directly with MIOS: no changes are necessary, the waveforms are not inverted like assumed (instead one channel of my scope was inverted…) - everything is fine! 
In order to avoid additional confusion here some final infos:
Under http://www.rs-components.de a datasheet for STEC16B can be found where the terminals are shown in following order: C A B — this is different from my documentation, where I wrote “A C B” (thats the common pinning for ALPS encoders)
Link to the modified schematic:
http://www.ucapps.de/mbhp/mbhp_dinx4_16enc_alps_stec16b03.pdf
Some more words to the supported encoder modes (or types): MIOS (and MIDIbox16E) allows to use the rotary encoders with double resolution. But this feature only works with non-detented encoders, the detented ones would increment two or four times with every “click”. This has to be taken into account when configuring the hardware settings in mios_tables.inc:
;; --------------------------------------------------------------------------
;; In this table DIN pins have to be assigned to rotary encoders for the
;; MIOS_ENC driver
;;
;; up to 64 entries are provided
;;
;; The table must be terminated with an ENC_EOT entry. Unused entries should
;; be filled with ENC_EOT
;;
;; ENC_ENTRY provides following parameters
;; o first parameter: number of shift register - 1, 2, 3, ... 16
;; o second parameter: number of pin; since two pins are necessary
;; for each encoder, an even number is expected: 0, 2, 4 or 6
;; o the third parameter contains the encoder mode:
;; either MIOS_ENC_MODE_NON_DETENTED
;; or MIOS_ENC_MODE_DETENTED
;; or MIOS_ENC_MODE_DETENTED2
;;
;; Configuration Examples:
;; ENC_ENTRY 1, 0, MIOS_ENC_MODE_NON_DETENTED ; non-detented encoder at pin 0 and 1 of SR 1
;; ENC_ENTRY 1, 2, MIOS_ENC_MODE_DETENTED ; detented encoder at pin 2 and 3 of SR 1
;; ENC_ENTRY 9, 6, MIOS_ENC_MODE_NON_DETENTED ; non-detented encoder at pin 6 and 7 of SR 9
;; --------------------------------------------------------------------------
MIOS_ENC_PIN_TABLE
;; encoders 1-16
;; SR Pin Mode
ENC_ENTRY 13, 0, MIOS_ENC_MODE_NON_DETENTED ; V-Pot 1
ENC_ENTRY 13, 2, MIOS_ENC_MODE_NON_DETENTED ; V-Pot 2
ENC_ENTRY 13, 4, MIOS_ENC_MODE_NON_DETENTED ; V-Pot 3
ENC_ENTRY 13, 6, MIOS_ENC_MODE_NON_DETENTED ; V-Pot 4
ENC_ENTRY 14, 0, MIOS_ENC_MODE_NON_DETENTED ; V-Pot 5
ENC_ENTRY 14, 2, MIOS_ENC_MODE_NON_DETENTED ; V-Pot 6
ENC_ENTRY 14, 4, MIOS_ENC_MODE_NON_DETENTED ; V-Pot 7
ENC_ENTRY 14, 6, MIOS_ENC_MODE_NON_DETENTED ; V-Pot 8
ENC_ENTRY 15, 0, MIOS_ENC_MODE_DETENTED ; Jog-Wheel
ENC_EOT
And here a diagram which illustrates the waveforms:
Best Regards, Thorsten.