My guess here is that you may have actually overtightened the 3/8" compression nut
You were correct in NOT
using the brass ferrule (compression ring)... so that will not be the issue here.
The new 3/8" compression nut (from the new flexible toilet riser) should have been hand tightened plus a full turn or two...but you did not want to cinch it down tightly!! In fact, if overtightened to extreme can separate from the angle shutoff completely!!
You also have a packing nut at the new shutoff...after opening fully give that packing nut a cinch down to keep from leaking in the future!
You may also want to double check the joints ABOVE the 3/8" compression nut... SOMETIMES small leak from above shows up at the bottom nut... so take a piece of toilet paper and wrap it around the upper part of the closet riser and see if it gets wet.. if it does... problem is actually at the upper nut.
Anyway, sounds like you overtightened nut to me... and now you need to purchase A NEW Flexible closet riser...
Let me know what you think here TAV... MARK