I use VagCom on my 2002 Toledo TDI without problems.
I also use the Leon profile for the full Controller scan, as you say, there isn't one for Toledo.
I get a few controllers responding including Engine, Radio, Airbags, Climate, Central Conveinience (locking, Alarm etc).. A scan is shown below..
I wonder why yours is different..
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VAG-COM Version: Release 311.2-N
Chassis Type: 1M - Seat Leon
Scan: 01,02,03,08,15,17,19,22,35,46,56
Address 01 -------------------------------------------------------
Controller: 038 906 012 FK
Component: 1,9l R4 EDC G000SG 3357
Coding: 00002
Shop #: WSC 06402
VSSZZZ1MZ2R065xxx SEZ7Z0A1390xxx
No fault code found.
Address 03 -------------------------------------------------------
Controller: 1C0 907 379 K
Component: ASR FRONT MK60 0103
Coding: 0021505
Shop #: WSC 00001
No fault code found.
Address 08 -------------------------------------------------------
Controller: 1M0 820 043 D
Component: 1M-CLIMATRONIC X0605
Coding: 00044
Shop #: WSC 00046
No fault code found.
Skipping Address 15-Airbags
Address 17 -------------------------------------------------------
Controller: 1M0 920 922 D
Component: KOMBI+WEGFAHRSP VDO V02
Coding: 05422
Shop #: WSC 00000
VSSZZZ1MZ2R065xxx SEZ7Z0A1390xxx
No fault code found.
Address 19 -------------------------------------------------------
Controller: 6N0 909 901
Component: Gateway K<->CAN 0001
Coding: 00006
Shop #: WSC 06402
No fault code found.
Address 46 -------------------------------------------------------
Controller: 1C0 959 799 F
Component: 3M Komfortgerát HLO 0003
Coding: 00258
Shop #: WSC 06402
1 Fault Found:
01135 - Interior Monitoring Sensors
36-00 - Open Circuit
Address 56 -------------------------------------------------------
Controller: 1M0 035 186 D
Component: Radio 0001
Coding: 00403
Shop #: WSC 06402
No fault code found.
End -------------------------------------------------------