I have seen this a few times recently. Typically, I can drag cards from the Temporary Zone and drop them onto the top card of R&D to add the cards to the top of R&D. Sometimes this does not work, but I am still able to drop the cards onto R&D (as @StashAugustine said) by dropping them onto the text box object that contains the 'R&D' text.
I have been using Chrome, not sure of the exact version because of the frequent automatic updates. No plugins for Jinteki.
The issue does not seem to happen early in games. I don't know if there is some correlation to cards in the 'Removed from Game' area(s), turn counter/credit counters exceeding any particular value, or other odd interaction, or if it is just the consequence of cumulative probability that makes it much more likely to have happened by the 3rd or 4th Indexing instead of the 1st.