I have the same issue occuring. I have tried benetj suggest config but it does not work for me. I am using WP 3.4.2
I am get this as the last part of the page:
</div>
<p><a href="/wp-admin/admin.php?page=wpfilebase_manage">Go back</a></p><h2>Synchronisation</h2><p>Checking for file changes... done!</p><p>Searching for new files... <p>276 Files found, 27 new.</p><script type="text/javascript"><!--
var _pbr_bs=[];var _pbr_ds=[];var _pbr_ss=[];var _pbr_ws=[];var _pbr_dc=[];function _pbr_s(f,d){var e=(d/_pbr_ss[f]);if(_pbr_ds[f]){_pbr_ds[f].innerHTML=""+Math.round(e*100)+" %";}_pbr_bs[f].style.width=""+Math.round(e*_pbr_ws[f])+"px";var c=(e>=0.5);if(_pbr_ds[f]&&_pbr_dc[f]!=c){var a=(c?document.getElementById("_pbr_b"+f):_pbr_bs[f]);_pbr_ds[f].style.color=a.style.backgroundColor;_pbr_dc[f]=c}}function _pbr_i(e,d,a,b){_pbr_bs[e]=document.getElementById("_pbr_"+e);_pbr_ds[e]=document.getElementById("_pbr_d"+e);_pbr_dc[e]=false;_pbr_ss[e]=a;_pbr_ws[e]=b;_pbr_s(e,d)};
// --></script><div id="_pbr_b0" style="width:100px;height:20px;text-align:left;background-color:#FFF;overflow:hidden;border:1px solid #000;">
<div id="_pbr_d0" style="width:100px;height:20px;text-align:center;line-height:20px;position:absolute;z-index:3;color:#0C0;"></div><div id="_pbr_0" style="width:0px;height:20px;background-color:#0C0;"></div>
</div><script>_pbr_i(0,0,27,100);</script>
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