In the most general sense, the "loophole" is plain old antisemtism. But I imagine you want something more specific.
In order to be nominated for membership in UN bodies like the Security Council or the Economic and Social Council, the nomination must come from a regional group. Israel's most natural regional group, the Asian Group, has been blocked by the Arab states. In recent years there has been a move to get Israel into the Western European and Others Group, which would allow it to become a member. A number of the European countries have been dragging their feet on this issue, despite pressure from the US.
Here is a quote from a Jerusalem Post story in 1999:
A report prepared at Israel's request by Sir Robert Jennings, president of the United Nations International Court of Justice until 1994, could help Israel finally gain admittance to one of the UN's five regional bodies.
Israel, excluded since its establishment from the groups - and thus effectively barred from joining the rotation for non-permanent seats on the Security Council - has long desired to be allowed into the 27-member Western European and Others Group (WEOG).
The Jennings report called on the WEOG to accept Israel as a member, describing its exclusion as illegal, morally shocking, and a breach of the UN charter. 'The unlawfulness of the exclusion of Israel speaks for itself, it is no mere anomaly or irregularity,' states the report, which goes on to call the exclusion a 'grotesque breach' of UN articles.
'Our exclusion is illegal and contravenes the very charter of the United Nations,' stressed Alan Baker, legal adviser at the Foreign Ministry, who presented the Jennings report to reporters yesterday.
Israel is the only UN member to remain outside the regional group system. It has been denied admission to the regional group for Asia, its geographical home, because of objections by Arab and some Moslem states.
Israel's membership to the WEOG would require the approval of all 27 members. Baker said some European countries have voiced objections and reservations.