Jennie
The problem is basically with all boards and multiple projects. The skip break points setting doesn't have any effect.
This is something that I am now trying to get to the bottom of because it is starting to cause real problems in various product developments - in all cases the code runs normally and running between breakpoints is basically Ok , as is single stepping code, but as soon as the target is left to run the debugger starts losing connection.
This is something that I am seeing on a KL25, for example. All is find until I command a RUN and then I get this (note that the board is running correctly when it happens but the debugger seems to believe that it has halted it for some reason):

This means that it is no longer possible to pause the operation or set new breakpoints etc. It is only really possible to command a restart. Sometimes a restart command allows it to reset and begin again but often there are errors and it has to be disconnected to start from scratch again.
In the breakpoint window there is also this strange temporary breakpoint which the debugger "thinks" that it has hit (the second is a real breakpoint at the start of code to help stopping it run out of control after a restart command):

If I disable the strange breakpoint it still behaves the same. And if I command a restart it re-inserts the breakpoint in the list again.
The breakpoint address is in SRAM. It is very close to the stack pointer value that is loaded from the reset vector (which is 0x20002ff0), in fact 64 bytes lower than it.
I don't know where this breakpoint comes from or whether it is the cause of the difficulties but the fact is that it is IMPOSSIBLE to halt running code and this is the only hint that is coming from the debugger that is visible.
When the restart fails the error that is seen is :
Program received signal SIGTRAP, Trace/breakpoint trap.
Quit (expect signal SIGINT when the program is resumed)
Quit (expect signal SIGINT when the program is resumed)
Quit (expect signal SIGINT when the program is resumed)
Quit (expect signal SIGINT when the program is resumed)
This however seems to be a separate issue since it is random (doesn't always happen) but is possibly still related to the first issue in some way.
Regards
Mark
P.S. This is the connection message when downloading and stopping at the entry point.
Connection from "127.0.0.1" via 127.0.0.1
Copyright 2012 P&E Microcomputer Systems,Inc.
Command Line :D:\Freescale\KDS_v3\eclipse\plugins\com.pemicro.debug.gdbjtag.pne_2.3.6.201602211227\win32\pegdbserver_console -device=NXP_KL2x_KL25Z128M4 -startserver -singlesession -serverport=7224 -interface=OPENSDA -speed=5000 -port=USB1 -configfile=C:ø
CMD>RE
Initializing.
Target has been RESET and is active.
CMD>CM D:\Freescale\KDS_v3\eclipse\plugins\com.pemicro.debug.gdbjtag.pne_2.3.6.201602211227\win32\gdi\P&E\supportFiles_ARM\NXP\KL2x\freescale_kl25z128m4_1x32x32k_pflash.arp
Initializing.
Initialized.
;version 1.05, 06/02/2014, Copyright 2014 P&E Microcomputer Systems, Inc. All rights reserved. www.pemicro.com [mk_128k_n_pflash_m0]
;device freescale, kl25z128m4, 1x32x32k, desc=pflash
;begin_cs device=$00000000, length=$00020000, ram=$20000000
Loading programming algorithm ...
Done.
CMD>EM
Erasing.
Module has been erased.
Reloading programming algorithm ...
done.
CMD>PM
Programming.
Processing Object File Data ...
.
Programmed.
CMD>VC
Verifying object file CRC-16 to device ranges ...
block 00000000-000000BF ...
Ok.
block 00000400-00007430 ...
Ok.
block 00007434-0000744C ...
Ok.
Checksum Verification Successful. (Cumulative CRC-16=$5AFD)
CMD>RE
Initializing.
Target has been RESET and is active.
WARNING - NO RESET SCRIPT FILE HAS BEEN CONFIGURED TO RUN!!!
TO MODIFY THE RESET SCRIPT SETTINGS, USE THE FOLLOWING MENU OPTION:
CONFIGURATION -> AUTOMATED SCRIPT OPTIONS
Preset breakpoint encountered.
{