"And as we also say, use a good power supply."
This was originator of the problem. At first time we try to use medical 
approved 4A PWS.But this type has a fast current protection circuit, which 
detect 1ms 4A current peek as short circuit. 
So our advise is to use middle categhory PWS (we have success with MW 
GS15B-1P1J). 

"we have never lost a TPS5217C due to this issue"
This is understandable beacuse average application is one BBB alone. This 
require 2A PWS which have no chance to harm TPS in this way.  
But in case of our special application more 5VDC powered device work 
together. This can be 2 or more BBB and more other device. This is why we 
try to use 4A or higher current PWS. This can demage TPS at startup. 

"I am not sure how to prevent caps from needing to be charged"
You dont need it! 
First what need to be learn by power rail diesigner is the rule: capacitive 
load on output of power regulator is very sensitive area. This is why power 
regulator manufacturer (including TI) using pages to explain its 
calculation. 
Loading reagulator with high/low/good/bad capcitor have diffrent effect to 
stabilized power rail. 
At first impression 100uF at position C34 is very high for regulator output 
(ext PWS). The 22uF with ESR=20mOhm (TI rec.) limit startup peak to normal 
value.
Moreover I cant known philosophy of USB host interface designer, why need 
100uF at IN of PDS? All AN of TPS20x1 PDS are recomend 0,1 to 10uF at this 
position except "Typical Hot-Plug Implemantation" where 1000uF applied. But 
this is not match, beacuse you cannot Hot-Plug USB host interface to BBB 
beacuse it is hardwired. 
I think it is some missplacing of this capacitor. USB 1.1 require ~100uF at 
downsteram port. But this capcitor must be connceted at output of TPS20x1 
not at input of. This provide a soft charge for system power rail. At input 
need just <=10uF. 

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