@divergreg: I know it looks like a cheap answer. BUT, all in all, majority of online security software will simply alert you when they detect an eval with a base64_decode command, because -except for very specific cases- they can’t decode and follow links or commands to see if it is dangerous. That’s why those are ending in the mere alert. WordFence firewall and scan plugin also has this behaviour. It’s up to you to further investigate and detect weird files and/or behaviours.
You should decompress in your PC the plugin zip pack downloaded from WP repo and FTP it to your “compromised” site. See if right after upload the files size has been increased compared to your offline versions (this due to code injection by a malware). If not, wait a couple minutes and compare again. If not, wait a couple hours and compare again. If not, and if after 24 hours the files remain untouched, you could then have peace of mind…