I've also noticed that the download procedure is slightly different between the hello world example and the SDK 2.0 version.
The hello_world (1.3) version:
Target interface speed set to 30 kHz
Resetting target
Halting target CPU...
...Target halted (PC = 0x00000540)
R0 = 00000000, R1 = 00000000, R2 = 00000000, R3 = 00000000
R4 = 00000000, R5 = 00000000, R6 = 00000000, R7 = 00000000
R8 = 00000000, R9 = 00000000, R10= 00000000, R11= 00000000
R12= 00000000, R13= 20030000, MSP= 20030000, PSP= 00000000
R14(LR) = FFFFFFFF, R15(PC) = 00000540
XPSR 01000000, APSR 00000000, EPSR 01000000, IPSR 00000000
CFBP 00000000, CONTROL 00, FAULTMASK 00, BASEPRI 00, PRIMASK 00
Reading all registers
Select auto target interface speed (1429 kHz)
Flash breakpoints enabled
Semi-hosting enabled (Handle on BKPT)
Wrong client mask. Semihosting I/O not changed.
Failed to disable SWO.
Failed to enable SWO. Could not determine a suitable SWO speed!
Downloading 1024 bytes @ address 0x00000000 - Verified OK
Downloading 16 bytes @ address 0x00000400 - Verified OK
Downloading 16096 bytes @ address 0x00000410 - Verified OK
Downloading 1596 bytes @ address 0x000042F0 - Verified OK
Downloading 8 bytes @ address 0x0000492C - Verified OK
Downloading 4 bytes @ address 0x00004934 - Verified OK
Downloading 4 bytes @ address 0x00004938 - Verified OK
Downloading 116 bytes @ address 0x0000493C - Verified OK
Writing register (PC = 0x000004d8)
Read 4 bytes @ address 0x000004D8 (Data = 0xF000B672)
Resetting target
Halting target CPU...
...Target halted (PC = 0x000004D8)
Read 2 bytes @ address 0x000011FA (Data = 0x2300)
Read 2 bytes @ address 0x000011FA (Data = 0x2300)
Read 2 bytes @ address 0x000011FA (Data = 0x2300)
R0 = 00000000, R1 = 00000000, R2 = 00000000, R3 = 00000000
R4 = 00000000, R5 = 00000000, R6 = 00000000, R7 = 00000000
R8 = 00000000, R9 = 00000000, R10= 00000000, R11= 00000000
R12= 00000000, R13= 20030000, MSP= 20030000, PSP= 00000000
R14(LR) = FFFFFFFF, R15(PC) = 000004D8
XPSR 01000000, APSR 00000000, EPSR 01000000, IPSR 00000000
CFBP 00000000, CONTROL 00, FAULTMASK 00, BASEPRI 00, PRIMASK 00
Reading all registers
Read 4 bytes @ address 0x000004D8 (Data = 0xF000B672)
Setting breakpoint @ address 0x000011FA, Size = 2, BPHandle = 0x0001
Starting target CPU...
...Breakpoint reached @ address 0x000011FA
Reading all registers
Removing breakpoint @ address 0x000011FA, Size = 2
Read 4 bytes @ address 0x000011FA (Data = 0x60FB2300)
Reading 64 bytes @ address 0x2002FFC0
Starting target CPU...
The 2.0 version:
Target interface speed set to 1000 kHz
Resetting target
Halting target CPU...
...Target halted (PC = 0x000004D8)
R0 = 00000000, R1 = 00000000, R2 = 00000000, R3 = 00000000
R4 = 00000000, R5 = 00000000, R6 = 00000000, R7 = 00000000
R8 = 00000000, R9 = 00000000, R10= 00000000, R11= 00000000
R12= 00000000, R13= 20030000, MSP= 20030000, PSP= 00000000
R14(LR) = FFFFFFFF, R15(PC) = 000004D8
XPSR 01000000, APSR 00000000, EPSR 01000000, IPSR 00000000
CFBP 00000000, CONTROL 00, FAULTMASK 00, BASEPRI 00, PRIMASK 00
Reading all registers
Select auto target interface speed (1429 kHz)
Flash breakpoints enabled
Semi-hosting enabled (Handle on BKPT)
Wrong client mask. Semihosting I/O not changed.
Failed to disable SWO.
Failed to enable SWO. Could not determine a suitable SWO speed!
Downloading 1024 bytes @ address 0x00000000 - Verified OK
Downloading 16 bytes @ address 0x00000400 - Verified OK
Downloading 16112 bytes @ address 0x00000410 - Verified OK
Downloading 13712 bytes @ address 0x00004300 - Verified OK
Downloading 8 bytes @ address 0x00007890 - Verified OK
Downloading 4 bytes @ address 0x00007898 - Verified OK
Downloading 4 bytes @ address 0x0000789C - Verified OK
Downloading 392 bytes @ address 0x000078A0 - Verified OK
Comparing flash [....................] Done.
Erasing flash [....................] Done.
Programming flash [....................] Done.
Verifying flash [....................] Done.
Writing register (PC = 0x00000540)
Read 4 bytes @ address 0x00000540 (Data = 0x4809B672)
Read 2 bytes @ address 0x000024DA (Data = 0xF002)
Read 2 bytes @ address 0x000024DA (Data = 0xF002)
Resetting target
Halting target CPU...
...Target halted (PC = 0x00000540)
Read 2 bytes @ address 0x000024DA (Data = 0xF002)
Read 2 bytes @ address 0x000024DA (Data = 0xF002)
Read 2 bytes @ address 0x000024DA (Data = 0xF002)
R0 = 00000000, R1 = 00000000, R2 = 00000000, R3 = 00000000
R4 = 00000000, R5 = 00000000, R6 = 00000000, R7 = 00000000
R8 = 00000000, R9 = 00000000, R10= 00000000, R11= 00000000
R12= 00000000, R13= 20030000, MSP= 20030000, PSP= 00000000
R14(LR) = FFFFFFFF, R15(PC) = 00000540
XPSR 01000000, APSR 00000000, EPSR 01000000, IPSR 00000000
CFBP 00000000, CONTROL 00, FAULTMASK 00, BASEPRI 00, PRIMASK 00
Reading all registers
Read 4 bytes @ address 0x00000540 (Data = 0x4809B672)
Setting breakpoint @ address 0x000024DA, Size = 2, BPHandle = 0x0001
Starting target CPU...
Comparing flash [....................] Done.
Erasing flash [....................] Done.
Programming flash [....................] Done.
Verifying flash [....................] Done.
...Breakpoint reached @ address 0x000024DA
Reading all registers
Removing breakpoint @ address 0x000024DA, Size = 2
Read 4 bytes @ address 0x000024DA (Data = 0xFE77F002)
Reading 64 bytes @ address 0x2002FFC0
Starting target CPU...
Note that in the 2.0 version there's some flash stuff going on (comparing, erasing, programming, verifying) where in 1.3 that isn't done. Could that have something to do with the problem?