Remove high-speed noise from power supply
When decoupling the use of parallel capacitors with values that are decade apart is like playing russian roulette. That is because you will get a resonant spike when the network with the bigger capacitor has become inductive and the network with smaller capacitor is still capacitive. I don't know if this is the problem here but maybe you should try replacing all the capacitors with one value either 10 or 100n. I did fast ltspice simulation to illustrate my point.

This is impedance with two different value capacitors connected by traces with identical inductances.


And this is impedance with identical capacitor values.

Edit: Here is the simulation file as requested in comments:

Version 4
SHEET 1 880 680
WIRE 208 208 -16 208
WIRE 304 208 208 208
WIRE 208 240 208 208
WIRE 304 240 304 208
WIRE -16 336 -16 208
WIRE 208 336 208 304
WIRE 304 336 304 304
WIRE -16 480 -16 416
WIRE 16 480 -16 480
WIRE 208 480 208 416
WIRE 208 480 16 480
WIRE 304 480 304 416
WIRE 304 480 208 480
WIRE 16 544 16 480
FLAG 16 544 0
SYMBOL voltage -16 320 R0
SYMATTR InstName V1
SYMATTR Value ""
SYMATTR Value2 AC 1 0
SYMBOL cap 192 240 R0
SYMATTR InstName C1
SYMATTR Value 100n
SYMBOL ind 192 320 R0
SYMATTR InstName L1
SYMATTR Value 3.5n
SYMBOL cap 288 240 R0
SYMATTR InstName C2
SYMATTR Value 10n
SYMBOL ind 288 320 R0
SYMATTR InstName L2
SYMATTR Value 3.5n
TEXT 432 256 Left 2 !.ac dec 1000 1 1000000000


The expression to plot is:V(n001)/I(V1).

Also I might not have understood correctly how you connected the capacitors but since inductance has a big influence here you should make sure that all the parallel caps are not connected through common but separate inductances. The motivation is that when connected in parallel the combined impedance of capacitance increases while the combined impedance of inductance reduces. So multiple capacitors having current flow through the same via is bad idea for decoupling purposes. Do whatever you can to avoid that.