I am having this same issue with a PPTP connection on iOS6.0.1 and 3G (iOS5 is ok for any connection, iOS6 is ok only for wifi).
1. This is part of the logfile (on the router) for wifi connection. VPN was connected.
Connect: ppp4 <--> /dev/pts/0
sent [LCP ConfReq id=0x1 <mru 1450> <asyncmap 0x0> <auth chap MS-v2> <magic 0xeea8d8f> <pcomp> <accomp>]
sent [LCP ConfReq id=0x1 <mru 1450> <asyncmap 0x0> <auth chap MS-v2> <magic 0xeea8d8f> <pcomp> <accomp>]
rcvd [LCP ConfReq id=0x1 <asyncmap 0x0> <magic 0x2f38b3a7> <pcomp> <accomp>]
sent [LCP ConfAck id=0x1 <asyncmap 0x0> <magic 0x2f38b3a7> <pcomp> <accomp>]
rcvd [LCP ConfReq id=0x1 <asyncmap 0x0> <magic 0x2f38b3a7> <pcomp> <accomp>]
sent [LCP ConfAck id=0x1 <asyncmap 0x0> <magic 0x2f38b3a7> <pcomp> <accomp>]
rcvd [LCP ConfAck id=0x1 <mru 1450> <asyncmap 0x0> <auth chap MS-v2> <magic 0xeea8d8f> <pcomp> <accomp>]
sent [LCP EchoReq id=0x0 magic=0xeea8d8f]
sent [CHAP Challenge id=0xdf <46fef03ba9f76d3ed8afecba4ffa0e09>, name = "*"]
rcvd [LCP EchoReq id=0x0 magic=0x2f38b3a7]
sent [LCP EchoRep id=0x0 magic=0xeea8d8f]
rcvd [LCP EchoRep id=0x0 magic=0x2f38b3a7]
rcvd [CHAP Response id=0xdf <d110d4287817312103b67f8a1bc1f45600000000000000002893318110d8a695c69595d433ced3 01fbd1bafeac2cd73200>, name = "Helga"]
sent [CHAP Success id=0xdf "S=F0186B350F8980D2B427D24A7C6A50C1DC872C9E M=Access granted"]
...
2. This is part of the logfile for 3G connection. VPN was refused.
Connect: ppp5 <--> /dev/pts/1
sent [LCP ConfReq id=0x1 <mru 1450> <asyncmap 0x0> <auth chap MS-v2> <magic 0x2a115525> <pcomp> <accomp>]
rcvd [LCP ConfReq id=0x1 <asyncmap 0x0> <magic 0x4b106103> <pcomp> <accomp>]
sent [LCP ConfAck id=0x1 <asyncmap 0x0> <magic 0x4b106103> <pcomp> <accomp>]
rcvd [LCP ConfRej id=0x1 <auth chap MS-v2>]
sent [LCP ConfReq id=0x2 <mru 1450> <asyncmap 0x0> <magic 0x2a115525> <pcomp> <accomp>]
rcvd [LCP ConfAck id=0x2 <mru 1450> <asyncmap 0x0> <magic 0x2a115525> <pcomp> <accomp>]
sent [LCP EchoReq id=0x0 magic=0x2a115525]
peer refused to authenticate: terminating link
sent [LCP TermReq id=0x3 "peer refused to authenticate"]
rcvd [LCP EchoReq id=0x0 magic=0x4b106103]
rcvd [LCP TermReq id=0x2 "MPPE required but not available"]
sent [LCP TermAck id=0x2]
Hangup (SIGHUP)
Modem hangup
Connection terminated.
I think the issue with buffering and reordering of received packets on iOS6.
The packages are confused because are multirouting paths through 3G.