3d printer z axis motor get stuck in high speeds (GT2560)

Hi!

I don't know how to describe problem properly, therefore I take a video.

Long story short, I brought CTC Prusa i3 replica, changed several parts, installed Marlin 1.1.6 (printer come with GT2560 rev A motherboard), all work fine until one day Z axis motor start acting strange. What I do in video:
1. Z auto home - OK
2. Z 10mm UP - OK
3. Z 10mm UP - OK
4. Z 100mm UP - Fail
5. Z auto home - OK
6. Z 100mm UP - Fail
7. Z 100mm DOWN - Fail
X and Y axis looks like work fine. Looks like it fail, when try to move (rotate) longer time and reach specific speed. This happen both, with TMC2208 and original A4988 drivers.
When disconnect one motor (any), second motor little bit rotates with vibration. I try to change several Marlin config parameters but without luck (see below latest parameters)

What I change from original:
* Prusa MK2 extruder body with E3D V6 hotend
* Motor drivers TMC2208
* "quick" Z-axis rod
* Ultrabase hotbed
* Power supply 360W
* Marlin 1.1.6

I made these changes step by step and all works fine until got hotbed. When I install new hotbed, original power supply did not give enough power, when both, hotend and hotbed turned on, voltage dropped from 12V to ~11.3V. I made couple prints until burned hotbed fuse (also fuse socket become black). I ordered new power supply, change fuse and all started working again much smoother than before. I left printer with 10 hour print to couple days and when I returned, print was finished without any problem. After couple days I want to start new print and problem started.

Marlin config parameters what I change from original GT2560 config file:
#define DEFAULT_AXIS_STEPS_PER_UNIT { 80.32, 80, 399.4, 158 }
#define DEFAULT_MAX_FEEDRATE { 400, 400, 1, 45 }
#define DEFAULT_MAX_ACCELERATION { 4000, 4000, 20, 4000 }
#define HOMING_FEEDRATE_Z (8*60)

May be someone can point, how to fix this?

Why is the homing_Z feedrate 8 times faster than the max_feedrate for Z ( 1mm/s )? Usually homing is half of max_speed.

Because I try to do everything to decrease Z speed. As you see, Z home moves quite slowly

Little update
Got brand new GT2560 Rev A+, with Cura 3.2.1 works fine, but with Cura 15.04.3 repeats.
Also installed new Marlin 1.8, prints quicker and looks better quality than previous.

Looks like nobody can tel, what case this "stucking" issue

PS. On GT2560 Rev A+, compare with Rev A, they turned around socket shielding for LCD and SD connectors

Did you check motor currents?