Hi Arnaldo,
For me, the delay time are around 10 ms both for the internal clock and the clock configuration you have. Keep in mind that because it is using a number of nops to wait, the timing is in the ~10% range.
Below is the code for toggling the blue LED (PTD1) on the FRDM-KL25Z:
Default internal clock:

With your clock settings:

The number of wait cycles is based on the core clock:
| #define WAIT1_INSTR_CLOCK_HZ | CPU_CORE_CLK_HZ /* for Kinetis, use core clock as base for instruction execution */ |
Which 48MHz in that configuration:
| #define CPU_CORE_CLK_HZ | 48000000U /* Initial value of the core/system clock frequency in Hz. */ |
I know there was an issue with what clock to be used (it used the bus clock instead of the the core clock) in a very old Wait component (about 2 years ago).
Are you really using the latest version from SourceForge (see https://mcuoneclipse.com/2014/10/21/mcuoneclipse-releases-on-sourceforge/ )?
In any case, I have attached my test project so you can compare the code and component version numbers.
I hope this helps,
Erich
PS: I recommend to report issues in the GitHub tracking system here: Issues · ErichStyger/McuOnEclipse_PEx · GitHub