I think, these are two different topics:
1. js/index.php
Did your tracking code change after you updated? Did you check your current WP-Piwik settings (Tracking section)? Is js/index.php selected and shown in the preview textarea above? If js/index.php is not used, please try to save your tracking settings again and retry.
If still the wrong code is used, please post your current tracking code here. (Please put the code in between backticks.)
2. Ghostery
WP-Piwik can’t hide Piwik from Ghostery, because it adds Piwik’s tracking code (to hide, WP-Piwik has to use the PHP tracking API which is not supported). What WP-Piwik can do:
a) It can replace the default tracking code (containing piwik.js) by js/index.php, which also just delivers piwik.js but with compression and caching.
b) It can replace the default tracking code by wp-piwik/proxy/piwik.php (before 0.9.9.18: wp-piwik/piwik.php), which hides your Piwik’s location but does not hide the tracking itself.
Maybe the version extension (js/index.php/0.9.9.x) disguised Piwik? But this extension caused other issues, so it was removed again. Apart from that, I’m quite sure Ghostery would also block this sooner or later.
Maybe Ghostery just updated its library to identify js/index.php, too. There are so many indicators Ghostery can use (e.g., look for _paq.push(['trackPageView']);
or check the piwik.js / js/index.php / proxy/piwik.php contents)…
Anyway, if (WP-)Piwik wasn’t identified by Ghostery before, this was a fortunate coincidence and never intended.