Ltspice - Simulation problem of cross regulation in a multiple output flyback
What you have there is not a multiple output flyback, but a simple one secondary transformer with two loads. You also have a few quirks that the SPICE world, in general, doesn't like. One of them is not setting vh for the VCSW. As the good book says (LTspice &gt; Circuit Elements &gt; S. ..., emphasis mine):

If Vh is zero, the switch is always completely on or off depending upon whether the input voltage is above the threshold. If Vh is positive, the switch shows hysteresis, as if it was controlled by a Schmitt trigger with trip points at Vt - Vh and Vt + Vh. [...] If Vh is negative, the switch will smoothly transition between the on and off impedances.

That smooth transition ensures that the derivatives are smooth and the engine doesn't cough &quot;timestep too small&quot; errors, or similar. The solution is simple: set vh&lt;0. The same for diodes:

The parameters epsilon and revepsilon can be specified to smoothly switch between the off and conducting states.

Some other tweaks won't hurt, such as Rser for capacitors or voltage sources, a few changes to make it a true multiple output and a minor adjustment to the value of the leakage inductance (note that I used the formula for 1 pri - 1 sec) and, overall, this is the result that works for me:

And the source (careful with wrapping):
Version 4
SHEET 1 880 680
WIRE 544 -112 480 -112
WIRE 672 -112 608 -112
WIRE 736 -112 672 -112
WIRE 768 -112 736 -112
WIRE 480 -80 480 -112
WIRE 672 -80 672 -112
WIRE 768 -80 768 -112
WIRE 160 -16 -96 -16
WIRE 256 -16 160 -16
WIRE -96 0 -96 -16
WIRE 256 0 256 -16
WIRE 160 16 160 -16
WIRE 480 32 480 0
WIRE 608 32 480 32
WIRE 672 32 672 -16
WIRE 672 32 608 32
WIRE 768 32 768 0
WIRE 768 32 672 32
WIRE 544 96 480 96
WIRE 672 96 608 96
WIRE 736 96 672 96
WIRE 768 96 736 96
WIRE 480 128 480 96
WIRE 672 128 672 96
WIRE 768 128 768 96
WIRE 160 160 160 80
WIRE 256 160 256 80
WIRE 256 160 160 160
WIRE 304 160 256 160
WIRE 352 160 304 160
WIRE 256 192 256 160
WIRE 352 192 352 160
WIRE 208 208 64 208
WIRE 480 240 480 208
WIRE 608 240 480 240
WIRE 672 240 672 192
WIRE 672 240 608 240
WIRE 768 240 768 208
WIRE 768 240 672 240
FLAG -96 80 0
FLAG 64 288 0
FLAG 208 256 0
FLAG 256 272 0
FLAG 352 256 0
FLAG 608 32 0
FLAG 608 240 0
FLAG 736 -112 o1
FLAG 736 96 o2
FLAG 304 160 d
SYMBOL voltage 64 192 R0
WINDOW 3 22 111 Left 2
SYMATTR InstName V1
SYMATTR Value pulse 0 1 0 {tr} {tr} {Ton} {T}
SYMBOL voltage -96 -16 R0
SYMATTR InstName V2
SYMATTR Value 50
SYMBOL sw 256 288 M180
SYMATTR InstName S1
SYMBOL diode 336 256 M180
WINDOW 0 24 64 Left 2
WINDOW 3 24 0 Left 2
SYMATTR InstName D1
SYMBOL ind2 240 -16 R0
SYMATTR InstName L1
SYMATTR Value {L}
SYMATTR Type ind
SYMBOL ind2 496 16 R180
WINDOW 0 36 80 Left 2
WINDOW 3 36 40 Left 2
SYMATTR InstName L2
SYMATTR Value {L}
SYMATTR Type ind
SYMBOL TVSdiode 144 16 R0
SYMATTR InstName D2
SYMATTR Value tvs
SYMBOL diode 544 -128 M90
WINDOW 0 0 32 VBottom 2
WINDOW 3 32 32 VTop 2
SYMATTR InstName D3
SYMBOL cap 656 -80 R0
WINDOW 123 23 79 Left 2
SYMATTR InstName C1
SYMATTR Value 5u
SYMATTR Value2 Rser=10m
SYMBOL res 752 -96 R0
SYMATTR InstName R1
SYMATTR Value 20
SYMBOL ind2 496 224 R180
WINDOW 0 36 80 Left 2
WINDOW 3 36 40 Left 2
SYMATTR InstName L3
SYMATTR Value {L}
SYMATTR Type ind
SYMBOL diode 544 80 M90
WINDOW 0 0 32 VBottom 2
WINDOW 3 32 32 VTop 2
SYMATTR InstName D4
SYMBOL cap 656 128 R0
WINDOW 123 23 79 Left 2
SYMATTR InstName C2
SYMATTR Value 5u
SYMATTR Value2 Rser=10m
SYMBOL res 752 112 R0
SYMATTR InstName R2
SYMATTR Value 20
TEXT 208 -64 Left 2 !k l1 l2 l3 {cpl}
TEXT -56 -200 Left 2 !.parma L=500u Lleak=5u cpl=sqrt(1-Lleak/L)\n+ f=100k T=1/f Ton=D*T-tr tr=T/1000 D=0.2
TEXT -56 -120 Left 2 !.tran {100/f}
TEXT -56 -296 Left 2 !.model sw sw ron=10m roff=10meg vt=0.5 vh=-0.5\n.model d d ron=10m roff=10meg vfwd=0.7 vrev=1k epsilon=0.1 revepsilon=50m\n.model tvs d ron=0.1 roff=10meg vfwd=100 vrev=100 epsilon=1 revepsilon=1